The cause of JBAS-5625 is a race between the HDScanner seeing the testEjb3xDeployment.jar and the test removing the jar. Its happening between stop of the deployment, and its removal. During this period it should not be exposed to the HDScanner, so there is a bug in the profile service repository/profile.getModifiedDeployments().

2008-09-01 01:40:55,515 DEBUG [org.jboss.profileservice.management.upload.remoting.DeployHandler] (WorkerThread#0[10.18.34.175:49212]) invoke, payload:

{DeploymentTargetID=names=[testEjb3xDeployment.jar]phase=APPLICATIONcopyContent=truedescription=null, clientAddress=/10.18.34.175}, parameter: stop2008-09-01 01:40:55,515 INFO [org.jboss.profileservice.management.upload.remoting.DeployHandler] (WorkerThread#0[10.18.34.175:49212]) Stop, [testEjb3xDeployment.jar]
...
2008-09-01 01:40:55,667 DEBUG [org.jboss.deployers.plugins.deployers.DeployersImpl] (WorkerThread#0[10.18.34.175:49212]) Fully Undeployed vfszip:/qa/services/hudson/hudson_workspace/workspace/JBoss-AS-5.0.x-TestSuite-sun15/trunk/build/output/jboss-5.0.0.CR2/server/profileservice/deploy/testEjb3xDeployment.jar
...
2008-09-01 01:40:55,701 DEBUG [org.jboss.system.server.profileservice.repository.SerializableDeploymentRepository] (HDScanner) Created deployment: AbstractVFSDeployment(testEjb3xDeployment.jar)
...
2008-09-01 01:40:55,716 DEBUG [org.jboss.profileservice.management.upload.remoting.DeployHandler] (WorkerThread#0[10.18.34.175:49214]) invoke, payload: {DeploymentTargetID=names=[testEjb3xDeployment.jar]phase=APPLICATIONcopyContent=truedescription=null, clientAddress=/10.18.34.175}

, parameter: undeploy
2008-09-01 01:40:55,716 INFO [org.jboss.profileservice.management.upload.remoting.DeployHandler] (WorkerThread#0[10.18.34.175:49214]) Undeploy, [testEjb3xDeployment.jar]
2008-09-01 01:40:55,718 INFO [org.jboss.profileservice.management.upload.remoting.DeployHandler] (WorkerThread#0[10.18.34.175:49214]) Undeployed: testEjb3xDeployment.jar
...
2008-09-01 01:40:55,728 DEBUG [org.jboss.deployment.OptAnnotationMetaDataDeployer] (HDScanner) Error during deploy: vfszip:/qa/services/hudson/hudson_workspace/workspace/JBoss-AS-5.0.x-TestSuite-sun15/trunk/build/output/jboss-5.0.0.CR2/server/profileservice/deploy/testEjb3xDeployment.jar
org.jboss.deployers.spi.DeploymentException: Cannot process metadata
at org.jboss.deployers.spi.DeploymentException.rethrowAsDeploymentException(DeploymentException.java:49)
at org.jboss.deployment.AnnotationMetaDataDeployer.deploy(AnnotationMetaDataDeployer.java:181)
at org.jboss.deployment.AnnotationMetaDataDeployer.deploy(AnnotationMetaDataDeployer.java:93)
at org.jboss.deployers.plugins.deployers.DeployerWrapper.deploy(DeployerWrapper.java:169)
...
Caused by: java.util.zip.ZipException: error in opening zip file
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:203)
at java.util.zip.ZipFile.<init>(ZipFile.java:234)
at org.jboss.virtual.plugins.context.zip.ZipFileWrapper.ensureZipFile(ZipFileWrapper.java:173)
at org.jboss.virtual.plugins.context.zip.ZipFileWrapper.openStream(ZipFileWrapper.java:207)
at org.jboss.virtual.plugins.context.zip.ZipEntryContext.openStream(ZipEntryContext.java:906)
...