First, you should not normally have to package your EAR differently. (This problem is not related to your EAR.) Note that Java EE 6 imposes stricter rules about what JARs in the EAR should be visible to the modules - such as app clients - in the module. And GlassFish 3 implements these stricter rules. Again, that is not causing this problem. You should just be aware of the changed rules.
Second, this is the same problem noted here:
http://forums.java.net/jive/message.jspa?messageID=471242#471242
See my reply there about clearing the Java Web Start cache of the GlassFish-related JARs and then relaunching. And please let us know if that clears up the problem.
- Tim
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