WebSphere Studio Workbench (WSWB) comes with the IBM 1.3.1 SR6A (Sidecar) JRE. This configuration actually includes two Java Virtual Machines (JVMs). The standard VM and the J9 VM. For the purposes of WSWB, you should use only the J9 VM.
Since the Java executable (e.g., java.exe) uses the standard VM is the default, you must pass the executable a VM argument telling it to use J9. Use the following command line to run Eclipse on Sidecar/J9.
eclipse.exe -vmargs -Xj9
If you are developing plugins for use on WSWB, you should update your runtime-workspace launch configurations to include the new VM argument. That is, put "-Xj9" in the VM arguments part of the launch configuration dialog.
If you are running Eclipse from a launcher or other program, ensure that you program passes the specified arguments to the Eclipse launcher.
From inside Eclipse you can tell if J9 is being used by consulting Help->About->Configuration Details. In this view there are various property key/value pairs which refer to VM levels. For example,
java.fullversion=J2RE 1.3.1 IBM J9 build 20031201 (JIT enabled)
java.vm.name=IBM J9SE VM
If you do not see "J9" in there, you are not running it. Please recheck your VM arguments.
If you should be asked for the version of J9 you are running, you can consult these properties or use
java -Xj9 -version
The chances that a problem you are encountering is a VM problem are slim. If you encounter a problem and you suspect is VM related you should try to recreate the problem on a different VM. This can be done in several ways:
If you can only recreate the problem on the J9 VM you should report the problem to the appropriate support group and include the J9 version (see above) as well as any other relevant details.