Another thing that comes to mind to try so see if you can get up and running is to make all of the JEE samples projects dependencies of the JEE test project. Should have the effect of making them all available to the TCCL down in the guts of the JEE processing. Not a long term solution but, assuming that this gets you any further alone (and I haven't tried this so don't know if it will actually improve things or not), it would at least allow you to run/debug some of the tests and get a feel for them.
Regards Simon
