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I have the same problem, using Java 1.6 update 29. The application starts with webstart, and clearing the cache did not help.
If clearing the cache does not help, you might see slightly different problem. So file a bug, attach full tracing to it. The full tracing could be obtained by include these line into <deployment-home>/deployment.properties file:
Tracing output are in the java console or in files under <deployment-home>/log.
You also might want to try latest build of 7u4 from http://jdk7.java.net/download.html just to see it fix the problem and include that info into the bug. If it does help, vote for the fix to be back-ported to 6.
We are using jre 1.6.0_17 and we didn't use the method InputStream.skip in our application. And we can resolve the problem by cleaning the cache. Before ask user to update their jre version, we need to make sure it's caused by the wrong version.