Why a classic asp + vb6 component application using MSXML6.0 is slower on W2K8 server compare to W2K3 server?

Recently we moved classic asp application+ vb6 com components from W2K3 server to W2K8 server.
The only change made in the vb6 component is upgrade from MSXML 2.0 to MSXML 6.0. These vb6 components are compiled into dlls and registered as COM components on the server.
The issue we are facing right now is that asp pages are taking a lot of time to load.
The functionality which used to take 8-10 sec is now taking around 40 seconds.
We inserted the logs and found that all the functions in vb6 code which are related to MSXML 6.0 upgrade have caused the slowness in the application.
On further research, we found that vb6 modules which uses 64 bit version of MSXML6.0(present under C:\Windows\System32) to load XML documents takes over two times longer to load an xml doc which uses 32bit version of MSXML6.0. (present under C:\Windows\sysWOW64)
Microsoft has provided a hotfix for this. Please see below url.
support.microsoft-com-kb-2799406
We already tried this hotfix but it did not fixed the performance issue.
Question:
1) On W2K8 machine, we are unable to use MSXML6.0 present under C:\Windows\sysWOW64. Whenever we try to reference to this location it by default references back to C:\Windows\system32. We also opened the vb project file in a notepad and changed the reference
location and opened the Project again but no success. Can anyone suggest what can be the probable solution to fix this?
Current Scenario:
Reference=*G{F5078F18-C551-11D3-89B9-0000F81FE221}#6.0#0#..WINDOWS-System32-msxml6.dll#Microsoft XML, v6.0
Expected Scenario:
Reference=*-G{F5078F18-C551-11D3-89B9-0000F81FE221}#6.0#0#..-WINDOWS-sysWOW64-msxml6.dll#Microsoft XML, v6.0
2) Once we compile this vb6 code to a dll by having a reference to this sysWOW64 folder, how to ensure/confirm reference from Syswow64 will be picked up once it will be on W2K8 server?
3) Also if you can suggest what can be other areas we should target/think of for resolving this performance issue?

I have encountered the exact same problem with msxml6.dll that is described in the latter part of you statement. Had you come up with a possible solution?

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    ---------------------------Stack Trace -------------------------------
    [04/Feb/2005:17:03:37] FINE ( 2260): for host 127.0.0.1 trying to POST /SmhsVisitingStudentWeb/visitingstudentdean, ntrans-j2ee reports: mapped uri "/visitingstudentdean" in context "/SmhsVisitingStudentWeb" to resource "visitingstudentdean"
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    [04/Feb/2005:17:03:37] FINE ( 2260): contextPath = /SmhsVisitingStudentWeb
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    [04/Feb/2005:17:03:37] FINE ( 2260): servletPath = null
    [04/Feb/2005:17:03:37] FINE ( 2260): pathInfo = null
    [04/Feb/2005:17:03:37] FINE ( 2260): SingleSignOn[server1]: Process request for '/SmhsVisitingStudentWeb/visitingstudentdean'
    [04/Feb/2005:17:03:37] FINE ( 2260): SingleSignOn[server1]: Checking for SSO cookie
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    [04/Feb/2005:17:03:37] FINEST ( 2260): In SimpleSFSBUUIDUtilImpl.createSessionKey() ++++++++ timeField = df664744 counterField = 1
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    [04/Feb/2005:17:03:37] FINE ( 2260): ++++ Entered SecClientRequestInterceptor::receive_reply
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    [04/Feb/2005:17:03:37] FINE ( 2260): Status to be set : 0
    [04/Feb/2005:17:03:37] FINE ( 2260): Invoked receivedReply()
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    [04/Feb/2005:17:03:37] FINE ( 2260): Status to be set : 0
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    [04/Feb/2005:17:03:37] FINEST ( 2260): NullSemaphore constructor() for PersistenceManagerImpl.fieldUpdateLock.
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    status = STATUS_NO_TRANSACTION
    Transaction Object = Transaction@18859698
    threads = 0
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    status = STATUS_NO_TRANSACTION
    Transaction Object = Transaction@18859698
    threads = 0
    ].begin:status = STATUS_NO_TRANSACTION ,txType: UNKNOWN for com.sun.jdo.spi.persistence.support.sqlstore.impl.PersistenceManagerImpl@15670a.
    [04/Feb/2005:17:03:37] FINEST ( 2260): Thread[service-j2ee-2,5,main] Tran[   Transaction:
    status = STATUS_NO_TRANSACTION
    Transaction Object = Transaction@18859698
    threads = 0
    ].setStatus: STATUS_NO_TRANSACTION => STATUS_ACTIVE for com.sun.jdo.spi.persistence.support.sqlstore.impl.PersistenceManagerImpl@15670a.
    [04/Feb/2005:17:03:37] FINEST ( 2260): Thread[service-j2ee-2,5,main] <->SQLPersistenceManagerFactory.getPersistenceManager() : com.sun.jdo.spi.persistence.support.sqlstore.impl.PersistenceManagerImpl@15670a for JTA: com.sun.ejb.containers.PMTransactionImpl@4.
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    query [55, (0/0), null, RD:null]
    classDef [56, (0/0), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    parameterDef [58, (0/0), null, RD:null]
    . [91, (1/10), null, RD:null]
    . [91, (1/5), null, RD:null]
    java [52, (1/1), null, RD:null]
    lang [52, (1/6), null, RD:null]
    String [52, (1/11), null, RD:null]
    _jdoParam1 [52, (1/18), null, RD:null]
    resultDef [83, (0/0), null, RD:null]
    this [5, (1/1), null, RD:null]
    filterDef [61, (0/0), null, RD:null]
    & [39, (1/32), null, RD:null]
    == [23, (1/17), null, RD:null]
    . [91, (1/7), null, RD:null]
    this [5, (1/3), null, RD:null]
    password [52, (1/8), null, RD:null]
    _jdoParam1 [52, (1/20), null, RD:null]
    == [23, (1/47), null, RD:null]
    . [91, (1/39), null, RD:null]
    this [5, (1/35), null, RD:null]
    active [52, (1/40), null, RD:null]
    true [18, (1/50), null, RD:null]
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    [04/Feb/2005:17:03:37] FINEST ( 2260): JQLC dump tree (typed AST)
    query [55, (0/0), null, RD:null]
    classDef [56, (0/0), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    parameterDef [58, (0/0), null, RD:null]
    java.lang.String [81, (1/10), java.lang.String, RD:null]
    _jdoParam1 [52, (1/18), java.lang.String, RD:null]
    resultDef [83, (0/0), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    this [5, (1/1), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    filterDef [61, (0/0), null, RD:null]
    & [39, (1/32), boolean, RD:null]
    == [23, (1/17), boolean, RD:null]
    this.password [71, (1/7), java.lang.String, RD:null]
    this [5, (1/3), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    password [52, (1/8), java.lang.String, RD:null]
    _jdoParam1 [80, (1/20), java.lang.String, RD:null]
    == [23, (1/47), boolean, RD:null]
    this.active [71, (1/39), java.lang.Boolean, RD:null]
    this [5, (1/35), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    active [52, (1/40), java.lang.Boolean, RD:null]
    true [18, (1/50), boolean, RD:null]
    [04/Feb/2005:17:03:37] FINER ( 2260): JQLC start optimizer
    [04/Feb/2005:17:03:37] FINEST ( 2260): JQLC dump tree (optimized AST)
    query [55, (0/0), null, RD:null]
    classDef [56, (0/0), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    parameterDef [58, (0/0), null, RD:null]
    java.lang.String [81, (1/10), java.lang.String, RD:null]
    _jdoParam1 [52, (1/18), java.lang.String, RD:null]
    resultDef [83, (0/0), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    this [5, (1/1), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    filterDef [61, (0/0), null, RD:null]
    & [39, (1/32), boolean, RD:null]
    == [23, (1/17), boolean, RD:null]
    this.password [71, (1/7), java.lang.String, RD:null]
    this [5, (1/3), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    password [52, (1/8), java.lang.String, RD:null]
    _jdoParam1 [80, (1/20), java.lang.String, RD:null]
    this.active [71, (1/39), java.lang.Boolean, RD:null]
    this [5, (1/35), gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState, RD:null]
    active [52, (1/40), java.lang.Boolean, RD:null]
    true [82, (1/50), boolean, RD:null]
    [04/Feb/2005:17:03:37] FINER ( 2260): JQLC start code generation
    [04/Feb/2005:17:03:37] FINER ( 2260): SQLStoreManager.getPersistenceConfig(), classType = gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState.
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    Verify that the schema file exists and that its contents are correct.
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    [04/Feb/2005:17:03:38] FINEST ( 2260): Thread[service-j2ee-2,5,main] Tran[   Transaction:
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    NestedException: com.sun.jdo.api.persistence.support.JDOUserException: The mapping for class gwumc.edu.ejb.smhs.visitingstudent.StudentBean129315485_JDOState is invalid. Compile the class in the IDE, correct any errors, and verify that all required files are packaged for execution.
         at com.sun.jdo.spi.persistence.support.sqlstore.SQLStoreManager.getPersistenceConfig(SQLStoreManager.java:145)
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