Portal EHP1 SP07 Patch causes app server jcontrol.exe to not start.....

I just finished patching our test portal system.
The database\message server which also has an app server on it starts up and runs just fine. The problem we are having is the second app server which is on a different windows host will not start (jcontrol.exe stays in a gray status).
Here is the developer trace errors for the second app server:
[Thr 5136] Wed Dec 08 06:56:19 2010
[Thr 5136] *** ERROR => invalid return code of process [bootstrap] (exitcode = 66) [jstartxx.c   1642]
[Thr 5136] JControlExecuteBootstrap: error executing bootstrap node [bootstrap] (rc = 66)
[Thr 5136] JControlCloseProgram: started (exitcode = 66)
[Thr 5136] JControlCloseProgram: good bye... (exitcode = 66)
Here is jvm_bootstrap.out log file located at \usr\sap\xxx\j00\work:
Bootstrap MODE:
<INSTANCE GLOBALS>
determined by parameter [ID0067689].
Exception occurred:
com.sap.engine.bootstrap.SynchronizationException: Database initialization failed! Check database properties!
     at com.sap.engine.bootstrap.Bootstrap.initDatabaseConnection(Bootstrap.java:422)
     at com.sap.engine.bootstrap.Bootstrap.<init>(Bootstrap.java:144)
     at com.sap.engine.bootstrap.Bootstrap.main(Bootstrap.java:814)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:331)
     at com.sap.engine.offline.OfflineToolStart.main(OfflineToolStart.java:81)
==[ Caused by: ]==----
com.sap.engine.frame.core.configuration.ConfigurationException: Error while connecting to DB.
     at com.sap.engine.core.configuration.impl.persistence.rdbms.DBConnectionPool.createConnection(DBConnectionPool.java:360)
     at com.sap.engine.core.configuration.impl.persistence.rdbms.DBConnectionPool.<init>(DBConnectionPool.java:125)
     at com.sap.engine.core.configuration.impl.persistence.rdbms.PersistenceHandler.<init>(PersistenceHandler.java:38)
     at com.sap.engine.core.configuration.impl.cache.ConfigurationCache.<init>(ConfigurationCache.java:149)
     at com.sap.engine.core.configuration.bootstrap.ConfigurationManagerBootstrapImpl.init(ConfigurationManagerBootstrapImpl.java:236)
     at com.sap.engine.core.configuration.bootstrap.ConfigurationManagerBootstrapImpl.<init>(ConfigurationManagerBootstrapImpl.java:49)
     at com.sap.engine.bootstrap.Synchronizer.<init>(Synchronizer.java:60)
     at com.sap.engine.bootstrap.Bootstrap.initDatabaseConnection(Bootstrap.java:419)
     at com.sap.engine.bootstrap.Bootstrap.<init>(Bootstrap.java:144)
     at com.sap.engine.bootstrap.Bootstrap.main(Bootstrap.java:814)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:331)
     at com.sap.engine.offline.OfflineToolStart.main(OfflineToolStart.java:81)
Caused by: com.sap.sql.log.OpenSQLException: Could not load class com.microsoft.sqlserver.jdbc.SQLServerDriver.
     at com.sap.sql.log.Syslog.createAndLogOpenSQLException(Syslog.java:106)
     at com.sap.sql.jdbc.NativeConnectionFactory.createNativeConnection(NativeConnectionFactory.java:143)
     at com.sap.sql.connect.OpenSQLDataSourceImpl.createPooledConnection(OpenSQLDataSourceImpl.java:608)
     at com.sap.sql.connect.OpenSQLDataSourceImpl.getPooledConnection(OpenSQLDataSourceImpl.java:285)
     at com.sap.engine.core.configuration.impl.persistence.rdbms.DBConnectionPool.createConnection(DBConnectionPool.java:302)
     ... 14 more
Caused by: java.lang.ClassNotFoundException: com.microsoft.sqlserver.jdbc.SQLServerDriver
     at com.sap.engine.offline.FileClassLoader.findClass(FileClassLoader.java:691)
     at com.sap.engine.offline.FileClassLoader.loadClass(FileClassLoader.java:600)
     at com.sap.engine.offline.FileClassLoader.loadClass(FileClassLoader.java:578)
     at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:303)
     at java.lang.Class.forName0(Native Method)
     at java.lang.Class.forName(Class.java:141)
     at com.sap.sql.jdbc.NativeConnectionFactory.createNativeConnection(NativeConnectionFactory.java:134)
     ... 17 more
[Bootstrap module]> Problem occurred while performing synchronization.
Any ideas?
Thank you,
Neil

Neil,
Thanks for your persistence and for reporting how you eventually solved it.  I had precisely the same problem after upgrading our production Portal from 7.00 to 7.01.  I didn't have problems in dev or test, because we don't have multiple app servers in those environments, just a central instance.  Now it's GoLive weekend and I've been pulling out my hair trying to get the app servers to work after the EHPI process is done.  I had to do just what you suggested, about editing the bootstrap configuration manually, as changes in the config tool didn't seem to have any effect on jcontrol.  I got that solved using your solution, but that led to nearly the same problem occurring for the individual dispatcher and server nodes, once jcontrol was started.  It took a while and lot of experimenting, but eventually I figured out that they were pulling the wrong jdbc driver from their individual configuration.manager properties (accessed via config tool).  The central instance was correctly updated by the EHPI program, but not the app servers.  Annoying!
Makes me wonder if I was supposed to leave the app servers running during the 'downtime' phase of the EHPI.  The manual, and the EHPI program, tell you at the start of the phase "shut down all dialog instances now", but then there's no indication of how these significant changes are supposed to be replicated to the app servers.  Several times I nearly escalated to a Very High priority Customer Message, but I kept unraveling the thread until I solved it, and your message here was the clue that put me on the right track.
Thanks,
Matt

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    CompilerOracle: exclude com/sap/engine/services/keystore/impl/security/CodeBasedSecurityConnector getApplicationDomain
    CompilerOracle: exclude com/sap/engine/services/rmi_p4/P4StubSkeletonGenerator generateStub
    CompilerOracle: exclude com/sapportals/portal/prt/util/StringUtils escapeToJS
    CompilerOracle: exclude com/sapportals/portal/prt/core/broker/PortalServiceItem startServices
    CompilerOracle: exclude com/sap/engine/services/webservices/server/deploy/WSConfigurationHandler downloadFile
    CompilerOracle: exclude com/sapportals/portal/prt/jndisupport/util/AbstractHierarchicalContext lookup
    [Thr 2940] JHVM_LoadJavaVM: Java VM created OK.
    JHVM_BuildArgumentList: main method arguments of node [server0 bootstrap]
    -> arg[  0]: com.sap.engine.bootstrap.Bootstrap
    -> arg[  1]: ./bootstrap
    -> arg[  2]: ID011962850
    [Thr 2940] Fri Feb 24 10:09:46 2006
    [Thr 2940] JHVM_RegisterNatives: registering methods in com.sap.bc.krn.perf.PerfTimes
    [Thr 2352] Fri Feb 24 10:09:49 2006
    [Thr 2352] JLaunchIExitJava: exit hook is called (rc = 0)
    [Thr 2352] JLaunchCloseProgram: good bye (exitcode = 0)
    dev_jcontrol:
    trc file: "C:\usr\sap\J2E\JC01\work\dev_jcontrol", trc level: 1, release: "700"
    node name   : jcontrol
    pid         : 3372
    system name : J2E
    system nr.  : 01
    started at  : Fri Feb 24 10:08:59 2006
    arguments       :
           arg[00] : C:\usr\sap\J2E\JC01\exe\jcontrol.EXE
           arg[01] : pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    [Thr 3396] Fri Feb 24 10:08:59 2006
    [Thr 3396] *** WARNING => INFO: Unknown property [instance.box.number=J2EJC01pc2389] [jstartxx.c   841]
    [Thr 3396] *** WARNING => INFO: Unknown property [instance.system.id=1] [jstartxx.c   841]
    JStartupReadInstanceProperties: read instance properties [C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties;C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties]
    -> ms host    : PC2389
    -> ms port    : 3900
    -> OS libs    : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> files [01] : C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties
    Instance properties
    -> ms host    : PC2389
    -> ms port    : 3900
    -> os libs    : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID11962800 : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID11962850 : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID11962800           : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [01] ID11962850           : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [02] sdm                  : C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties
    [Thr 3396] JControlExecuteBootstrap: execute bootstrap process [bootstrap]
    [Thr 3396] [Node: bootstrap] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [bootstrap]
    -> node name          : bootstrap
    -> node type          : bootstrap
    -> node execute       : yes
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    : -Djco.jarm=1
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 512M
    -> root path          : C:\usr\sap\J2E\JC01\j2ee\cluster
    -> class path         : .\bootstrap\launcher.jar
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : com.sap.engine.offline.OfflineToolStart
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> parameters         : com.sap.engine.bootstrap.Bootstrap ./bootstrap ID0119628
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 60000
    -> shutdown timeout   : 120000
    JControlStartJLaunch: program = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[00] = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[01] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> arg[02] = -DSAPINFO=J2E_01_bootstrap
    -> arg[03] = -nodeId=-1
    -> arg[04] = -file=C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> arg[05] = -syncSem=JSTARTUP_WAIT_ON_3372
    -> arg[06] = -nodeName=bootstrap
    -> arg[07] = -jvmOutFile=C:\usr\sap\J2E\JC01\work\jvm_bootstrap.out
    -> arg[08] = -stdOutFile=C:\usr\sap\J2E\JC01\work\std_bootstrap.out
    -> arg[09] = -locOutFile=C:\usr\sap\J2E\JC01\work\dev_bootstrap
    -> arg[10] = -mode=BOOTSTRAP
    -> arg[11] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> lib path = PATH=C:\j2sdk1.4.2_09\jre\bin\server;C:\j2sdk1.4.2_09\jre\bin;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    -> exe path = PATH=C:\j2sdk1.4.2_09\bin;C:\usr\sap\J2E\JC01\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    [Thr 3396] Fri Feb 24 10:09:37 2006
    [Thr 3396] JControlExecuteBootstrap: read instance values after global bootstrap
    [Thr 3396] *** WARNING => INFO: Unknown property [instance.box.number=J2EJC01pc2389] [jstartxx.c   841]
    [Thr 3396] *** WARNING => INFO: Unknown property [instance.system.id=1] [jstartxx.c   841]
    JStartupReadInstanceProperties: read instance properties [C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties;C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties]
    -> ms host    : PC2389
    -> ms port    : 3900
    -> OS libs    : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> Admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    [Thr 3396] JControlExecuteBootstrap: enumerate the nodes after global bootstrap
    Used property files
    -> files [00] : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> files [01] : C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties
    Instance properties
    -> ms host    : PC2389
    -> ms port    : 3900
    -> os libs    : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> admin URL  :
    -> run mode   : NORMAL
    -> run action : NONE
    -> enabled    : yes
    Bootstrap nodes
    -> [00] bootstrap            : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [01] bootstrap_ID11962800 : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [02] bootstrap_ID11962850 : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    Worker nodes
    -> [00] ID11962800           : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [01] ID11962850           : C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> [02] sdm                  : C:\usr\sap\J2E\JC01\SDM\program\config\sdm_jstartup.properties
    [Thr 3396] JControlExecuteBootstrap: execute bootstrap process [bootstrap_ID11962800]
    [Thr 3396] [Node: dispatcher bootstrap] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [bootstrap_ID11962800]
    -> node name          : dispatcher bootstrap
    -> node type          : bootstrap
    -> node execute       : yes
    -> jlaunch parameters :
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    : -Djco.jarm=1
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 64M
    -> root path          : C:\usr\sap\J2E\JC01\j2ee\cluster
    -> class path         : .\bootstrap\launcher.jar
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : com.sap.engine.offline.OfflineToolStart
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> parameters         : com.sap.engine.bootstrap.Bootstrap ./bootstrap ID011962800
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 60000
    -> shutdown timeout   : 120000
    JControlStartJLaunch: program = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[00] = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[01] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> arg[02] = -DSAPINFO=J2E_01_bootstrap
    -> arg[03] = -nodeId=-1
    -> arg[04] = -file=C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> arg[05] = -syncSem=JSTARTUP_WAIT_ON_3372
    -> arg[06] = -nodeName=bootstrap_ID11962800
    -> arg[07] = -jvmOutFile=C:\usr\sap\J2E\JC01\work\jvm_bootstrap_ID11962800.out
    -> arg[08] = -stdOutFile=C:\usr\sap\J2E\JC01\work\std_bootstrap_ID11962800.out
    -> arg[09] = -locOutFile=C:\usr\sap\J2E\JC01\work\dev_bootstrap_ID11962800
    -> arg[10] = -mode=BOOTSTRAP
    -> arg[11] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> lib path = PATH=C:\j2sdk1.4.2_09\jre\bin\server;C:\j2sdk1.4.2_09\jre\bin;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    -> exe path = PATH=C:\j2sdk1.4.2_09\bin;C:\usr\sap\J2E\JC01\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    [Thr 3396] Fri Feb 24 10:09:44 2006
    [Thr 3396] JControlExecuteBootstrap: execute bootstrap process [bootstrap_ID11962850]
    [Thr 3396] [Node: server0 bootstrap] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [bootstrap_ID11962850]
    -> node name          : server0 bootstrap
    -> node type          : bootstrap
    -> node execute       : yes
    -> jlaunch parameters :
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    : -Djco.jarm=1
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 512M
    -> root path          : C:\usr\sap\J2E\JC01\j2ee\cluster
    -> class path         : .\bootstrap\launcher.jar
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : com.sap.engine.offline.OfflineToolStart
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> parameters         : com.sap.engine.bootstrap.Bootstrap ./bootstrap ID011962850
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 60000
    -> shutdown timeout   : 120000
    JControlStartJLaunch: program = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[00] = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[01] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> arg[02] = -DSAPINFO=J2E_01_bootstrap
    -> arg[03] = -nodeId=-1
    -> arg[04] = -file=C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> arg[05] = -syncSem=JSTARTUP_WAIT_ON_3372
    -> arg[06] = -nodeName=bootstrap_ID11962850
    -> arg[07] = -jvmOutFile=C:\usr\sap\J2E\JC01\work\jvm_bootstrap_ID11962850.out
    -> arg[08] = -stdOutFile=C:\usr\sap\J2E\JC01\work\std_bootstrap_ID11962850.out
    -> arg[09] = -locOutFile=C:\usr\sap\J2E\JC01\work\dev_bootstrap_ID11962850
    -> arg[10] = -mode=BOOTSTRAP
    -> arg[11] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> lib path = PATH=C:\j2sdk1.4.2_09\jre\bin\server;C:\j2sdk1.4.2_09\jre\bin;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    -> exe path = PATH=C:\j2sdk1.4.2_09\bin;C:\usr\sap\J2E\JC01\j2ee\os_libs;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
    [Thr 3112] Fri Feb 24 10:09:51 2006
    [Thr 3112] JControlRequestFunc: Thread 3112 started as listener thread for np messages.
    [Thr 3396] JControlIBuildProcessList: Maximum error count is set to 4
    [Thr 3396] [Node: dispatcher] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [ID11962800]
    -> node name          : dispatcher
    -> node type          : dispatcher
    -> node execute       : yes
    -> jlaunch parameters :
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Djco.jarm=1 -XX:NewSize=10m -XX:MaxNewSize=10m -XX:+DisableExplicitGC -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 64M
    -> init heap size     : 64M
    -> root path          : C:\usr\sap\J2E\JC01\j2ee\cluster\dispatcher
    -> class path         : .\bin\boot\boot.jar;.\bin\system\bytecode.jar;.
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : com.sap.engine.boot.Start
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> parameters         :
    -> debuggable         : no
    -> debug mode         : no
    -> debug port         : 60000
    -> shutdown timeout   : 120000
    [Thr 3396] [Node: server0] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [ID11962850]
    -> node name          : server0
    -> node type          : server
    -> node execute       : yes
    -> jlaunch parameters :
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    : -Djava.security.policy=./java.policy -Djava.security.egd=file:/dev/urandom -Dorg.omg.CORBA.ORBClass=com.sap.engine.system.ORBProxy -Dorg.omg.CORBA.ORBSingletonClass=com.sap.engine.system.ORBSingletonProxy -Djavax.rmi.CORBA.PortableRemoteObjectClass=com.sap.engine.system.PortableRemoteObjectProxy -Dorg.xml.sax.driver=com.sap.engine.lib.xml.parser.SAXParser -Djco.jarm=1 -Dsun.io.useCanonCaches=false -XX:NewSize=85m -XX:MaxNewSize=85m -XX:MaxPermSize=192m -Djava.awt.headless=true -XX:PermSize=192m -XX:SurvivorRatio=2 -XX:TargetSurvivorRatio=90 -XX:SoftRefLRUPolicyMSPerMB=1 -verbose:gc -XX:DisableExplicitGC -XX:PrintGCDetails -XX:PrintGCTimeStamps -XX:UseParNewGC -Drdbms.driverLocation=c:/sapdb/programs/runtime/jar/sapdbc.jar
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 512M
    -> init heap size     : 512M
    -> root path          : C:\usr\sap\J2E\JC01\j2ee\cluster\server0
    -> class path         : .\bin\boot\boot.jar;.\bin\boot\jaas.jar;.\bin\system\bytecode.jar;.
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : com.sap.engine.boot.Start
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> parameters         :
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 50121
    -> shutdown timeout   : 120000
    [Thr 3396] [Node: SDM] java home is set by profile parameter
         Java Home: C:\j2sdk1.4.2_09
    [Thr 3396] JStartupICheckFrameworkPackage: can't find framework package C:\usr\sap\J2E\JC01\exe\jvmx.jar
    JStartupIReadSection: read node properties [sdm]
    -> node name          : SDM
    -> node type          : sdm
    -> node execute       : yes
    -> java path          : C:\j2sdk1.4.2_09
    -> java parameters    :
    -> java vm version    : 1.4.2_09-b05
    -> java vm vendor     : Java HotSpot(TM) Server VM (Sun Microsystems Inc.)
    -> java vm type       : server
    -> java vm cpu        : x86
    -> heap size          : 128M
    -> root path          : C:\usr\sap\J2E\JC01\SDM\program
    -> class path         : C:\usr\sap\J2E\JC01\SDM\program\bin\SDM.jar
    -> OS libs path       : C:\usr\sap\J2E\JC01\j2ee\os_libs
    -> main class         : SDMInternal
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : C:\usr\sap\J2E\JC01\exe\jstartup.jar;C:\usr\sap\J2E\JC01\exe\jvmx.jar
    -> shutdown class     : com.sap.sdm.jstartup.shutdown.InternalShutDown
    -> parameters         : server sdmhome=C:\usr\sap\J2E\JC01\SDM\program
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 60000
    -> shutdown timeout   : 120000
    [Thr 3396] JControlMSConnect: attached to message server (PC2389/3900)
    JControlStartJLaunch: program = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[00] = C:\usr\sap\J2E\JC01\exe\jlaunch.exe
    -> arg[01] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> arg[02] = -DSAPINFO=J2E_01_dispatcher
    -> arg[03] = -nodeId=0
    -> arg[04] = -file=C:\usr\sap\J2E\JC01\j2ee\cluster\instance.properties
    -> arg[05] = -syncSem=JSTARTUP_WAIT_ON_3372
    -> arg[06] = -nodeName=ID11962800
    -> arg[07] = -jvmOutFile=C:\usr\sap\J2E\JC01\work\jvm_dispatcher.out
    -> arg[08] = -stdOutFile=C:\usr\sap\J2E\JC01\work\std_dispatcher.out
    -> arg[09] = -locOutFile=C:\usr\sap\J2E\JC01\work\dev_dispatcher
    -> arg[10] = -mode=JCONTROL
    -> arg[11] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
    -> lib path = PATH=C:\j2sdk1.4.2_09\jre\bin\server;C:\j2sdk1.4.2_09\jre\bin;c:\sapdb\programs\bin;c:\sapdb\programs\pgm;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Adaptec Shared\System;C:\usr\sap\J2E\SYS\exe\uc\NTI386
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    -> arg[08] = -stdOutFile=C:\usr\sap\J2E\JC01\work\std_server0.out
    -> arg[09] = -locOutFile=C:\usr\sap\J2E\JC01\work\dev_server0
    -> arg[10] = -mode=JCONTROL
    -> arg[11] = pf=C:\usr\sap\J2E\SYS\profile\J2E_JC01_PC2389
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    -> java vm cpu        : amd64
    -> heap size          : 128M
    -> init heap size     : 128M
    -> root path          : ..\SMDAgent
    -> class path         : ..\..\exe\jstartupapi.jar;..\..\exe\jstartupimpl.jar;lib\patch_7.01.6.0.20100125105844\launcher\smdagentlauncher.jar
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    -> main class         : com.sap.smd.agent.launcher.SMDAgentLauncher
    -> framework class    : com.sap.bc.proj.jstartup.JStartupFramework
    -> registr. class     : com.sap.bc.proj.jstartup.JStartupNatives
    -> framework path     : ..\usr\sap\SMD\exe\jstartup.jar;..\usr\sap\SMD\exe\jvmx.jar
    -> parameters         : run jcontrol
    -> debuggable         : yes
    -> debug mode         : no
    -> debug port         : 58981
    -> shutdown timeout   : 20000
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    Current environment:
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    We have an open SR ticket with Support but as yet they have not been able to help us...

    Looks like Tuxedo is not doing he's job. You should double check the Tuxedo version and rolling patch installed.
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    Moreover, from your output it is difficult to understand what's going wrong.
    Nicolas.

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