Deployment destroys OC4j configuration

Sometimes the following problem occures during deplyoment from JDeveloper to oc4j:
We have a Webapp with JSPs, Servlets, Java classes and XSQL.
The deplyoment finish as usual and normally with exit code 0:
But the problem is the server.xml file and the http-web-site.xml are destroyed.
Is it a known bug?
We are using JDeveloper 9i Production (Windows XP) and an oc4j 9.0.2.0.0 on Solaris.
Thank you
Michael

I'm not sure whether you have the same problem as I have:
I deployed EAR from NWDS and log configuration didn't change even if I had created log-configuration.xml. Then I found this file in root of EAR instead of inside META-INF folder. I made manual modificaton to that and manually deployed. And configuration worked. Still I want to have correct deployment automatically from NWDS.

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    09/09/29 08:31:12 at oracle.bi.analytics.management.monitoring.PerfmonThr.<init>(PerfmonThr.java:47)
    09/09/29 08:31:12 at oracle.bi.analytics.management.Agent.registerPerformanceMBeans(Agent.java:87)
    09/09/29 08:31:12 at oracle.bi.analytics.management.Agent.registerMBeans(Agent.java:55)
    09/09/29 08:31:12 at oracle.bi.analytics.management.Oc4jAgent.registerMBeans(Oc4jAgent.java:48)
    09/09/29 08:31:12 at oracle.bi.analytics.management.Oc4jAgent.main(Oc4jAgent.java:26)
    09/09/29 08:31:12 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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    09/09/29 08:31:12 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
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    09/09/29 08:31:12 at java.lang.Thread.run(Thread.java:595)
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    09/09/29 08:31:14 xdo.server.config.dir = null
    09/09/29 08:31:14 BI Beans Graph version [9.9.9.40.4350]
    09/09/29 08:31:15 Oracle Containers for J2EE 10g (10.1.3.1.0) initialized
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    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].util.ReleasableResourcePooledExecutor$MyWorker.run(ReleasableResourcePooledExecutor.java:303)
    at java.lang.Thread.run(Thread.java:595)
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    java.lang.LinkageError: loader constraints violated when linking org/xml/sax/InputSource class
    at org.apache.axis.utils.XMLUtils.newDocument(XMLUtils.java:369)
    at org.apache.axis.utils.XMLUtils.newDocument(XMLUtils.java:388)
    at org.apache.axis.configuration.FileProvider.configureEngine(FileProvider.java:179)
    at org.apache.axis.AxisEngine.init(AxisEngine.java:172)
    at org.apache.axis.AxisEngine.<init>(AxisEngine.java:156)
    at org.apache.axis.server.AxisServer.<init>(AxisServer.java:88)
    at org.apache.axis.server.DefaultAxisServerFactory.createServer(DefaultAxisServerFactory.java:109)
    at org.apache.axis.server.DefaultAxisServerFactory.getServer(DefaultAxisServerFactory.java:73)
    at org.apache.axis.server.AxisServer.getServer(AxisServer.java:73)
    at org.apache.axis.transport.http.AxisServletBase.getEngine(AxisServletBase.java:185)
    at org.apache.axis.transport.http.AxisServletBase.getOption(AxisServletBase.java:396)
    at org.apache.axis.transport.http.AxisServletBase.init(AxisServletBase.java:112)
    at org.apache.axis.transport.http.AxisServlet.init(AxisServlet.java:156)
    at javax.servlet.GenericServlet.init(GenericServlet.java:256)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.loadServlet(HttpApplication.java:2361)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.findServlet(HttpApplication.java:4810)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.findServlet(HttpApplication.java:4734)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.getRequestDispatcher(HttpApplication.java:2957)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.doProcessRequest(HttpRequestHandler.java:736)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.processRequest(HttpRequestHandler.java:448)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.serveOneRequest(HttpRequestHandler.java:216)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.run(HttpRequestHandler.java:117)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.run(HttpRequestHandler.java:110)
    at oracle.oc4j.network.ServerSocketReadHandler$SafeRunnable.run(ServerSocketReadHandler.java:260)
    at oracle.oc4j.network.ServerSocketAcceptHandler.procClientSocket(ServerSocketAcceptHandler.java:239)
    at oracle.oc4j.network.ServerSocketAcceptHandler.access$700(ServerSocketAcceptHandler.java:34)
    at oracle.oc4j.network.ServerSocketAcceptHandler$AcceptHandlerHorse.run(ServerSocketAcceptHandler.java:880)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].util.ReleasableResourcePooledExecutor$MyWorker.run(ReleasableResourcePooledExecutor.java:303)
    at java.lang.Thread.run(Thread.java:595)
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    at org.apache.axis.utils.XMLUtils.newDocument(XMLUtils.java:369)
    at org.apache.axis.utils.XMLUtils.newDocument(XMLUtils.java:388)
    at org.apache.axis.configuration.FileProvider.configureEngine(FileProvider.java:179)
    at org.apache.axis.AxisEngine.init(AxisEngine.java:172)
    at org.apache.axis.AxisEngine.<init>(AxisEngine.java:156)
    at org.apache.axis.server.AxisServer.<init>(AxisServer.java:88)
    at org.apache.axis.server.DefaultAxisServerFactory.createServer(DefaultAxisServerFactory.java:109)
    at org.apache.axis.server.DefaultAxisServerFactory.getServer(DefaultAxisServerFactory.java:73)
    at org.apache.axis.server.AxisServer.getServer(AxisServer.java:73)
    at org.apache.axis.transport.http.AxisServletBase.getEngine(AxisServletBase.java:185)
    at org.apache.axis.transport.http.AxisServletBase.getOption(AxisServletBase.java:396)
    at org.apache.axis.transport.http.AxisServletBase.init(AxisServletBase.java:112)
    at org.apache.axis.transport.http.AxisServlet.init(AxisServlet.java:156)
    at javax.servlet.GenericServlet.init(GenericServlet.java:256)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.loadServlet(HttpApplication.java:2361)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.findServlet(HttpApplication.java:4810)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.findServlet(HttpApplication.java:4734)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpApplication.getRequestDispatcher(HttpApplication.java:2957)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.doProcessRequest(HttpRequestHandler.java:736)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.processRequest(HttpRequestHandler.java:448)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.serveOneRequest(HttpRequestHandler.java:216)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.run(HttpRequestHandler.java:117)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.HttpRequestHandler.run(HttpRequestHandler.java:110)
    at oracle.oc4j.network.ServerSocketReadHandler$SafeRunnable.run(ServerSocketReadHandler.java:260)
    at oracle.oc4j.network.ServerSocketAcceptHandler.procClientSocket(ServerSocketAcceptHandler.java:239)
    at oracle.oc4j.network.ServerSocketAcceptHandler.access$700(ServerSocketAcceptHandler.java:34)
    at oracle.oc4j.network.ServerSocketAcceptHandler$AcceptHandlerHorse.run(ServerSocketAcceptHandler.java:880)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].util.ReleasableResourcePooledExecutor$MyWorker.run(ReleasableResourcePooledExecutor.java:303)
    at java.lang.Thread.run(Thread.java:595)
    09/10/05 11:31:09.867 xmlpserver: Servlet error
    java.lang.LinkageError: loader constraints violated when linking org/xml/sax/ErrorHandler class
    at oracle.cabo.share.xml.TreeBuilder.parse(Unknown Source)
    at oracle.cabo.share.config.ApplicationConfigurationParser.createInstance(Unknown Source)
    at oracle.cabo.share.config.ApplicationConfiguration.getInstance(Unknown Source)
    at oracle.cabo.share.config.Configuration.getConfiguration(Unknown Source)
    at oracle.cabo.ui.ServletRenderingContext.__getConfiguration(Unknown Source)
    at oracle.cabo.ui.RootRenderingContext.getConfiguration(Unknown Source)
    at oracle.cabo.ui.RootRenderingContext._getLookAndFeelManager(Unknown Source)
    at oracle.cabo.ui.RootRenderingContext.getLookAndFeel(Unknown Source)
    at oracle.cabo.ui.ServletRenderingContext._getContentType(Unknown Source)
    at oracle.cabo.ui.ServletRenderingContext.prepareResponse(Unknown Source)
    at oracle.apps.xdo.servlet.ui.UIUtils.renderError(UIUtils.java:1142)
    at login.jspService(_login.java:368)
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    at oracle.jsp.runtimev2.JspPageTable.service(JspPageTable.java:453)
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    at javax.servlet.http.HttpServlet.service(HttpServlet.java:856)
    at com.evermind[Oracle Containers for J2EE 10g (10.1.3.1.0) ].server.http.ResourceFilterChain.doFilter(ResourceFilterChain.java:64)

    sorry, I think I'm mistaken. That error is what it says, but it's not going to stop publisher working (it's when systemsmanagement is initialising, so perfmon may not be available).
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    java.lang.LinkageError: loader constraints violated when linking org/xml/sax/InputSource classUnfortunately I have no idea what this means.
    Maybe try redeploying xmlpublisher, or using the latest version (10.1.3.4.1)?
    Does Presentation Services work, i.e. can you log in to Dashboards and Answers?

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    Here is a description of the problem we are having:
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    import ORG.oclc.da.beans.*;
    import javax.naming.*;
    import java.util.*;
    import java.rmi.*;
    import javax.ejb.*;
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         public static void main(String[] args)
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    <description>
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    </description>
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    <session>
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    <home>ORG.oclc.da.beans.DAServicesDemoHome</home>
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    <transaction-type>Container</transaction-type>
    </session>
    </enterprise-beans>
    <assembly-descriptor>
    <container-transaction>
    <method>
    <ejb-name>DAServicesDemo</ejb-name>
    <method-name>*</method-name>
    </method>
    <trans-attribute>NotSupported</trans-attribute>
    </container-transaction>
    </assembly-descriptor>
    </ejb-jar>
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    time="ea2215b915">
         <enterprise-beans>
              <session-deployment name="DAServicesDemo"
    location="DAServicesDemo"
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    persistence-filename="DAServicesDemo" />
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    Hi Jonathan,
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    Avi.

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