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The problem with GW and Java isn't necessarily the JRE from what I understand it's related to the awt toolkit and it's support for openGL.
The fix for groupwise is to run groupwise.sh - jvm=-Dawt.toolkit=sun.awt.motif.Mtoolkit . I think that changing the jvm from underneath GW technically does this. You have to use the 3/30/06 SP1 beta code for this to work. Of course Jason beat me to the punch on this...
So if you can find a way to start your app using the sun awt toolkit you might find success.
There is an additional workaround available for those that find the JRE does not work.
Modify the properties of the launcher to add the following startup switch:
This switch will ONLY work with GroupWise build 3/30/06 or later. Try http://gwcode.provo.novell.com/ for the this client.
Many thanks to Alex for supplying this switch, note that this is a temporary workaround only.