I'm doing concurrent IDL and Java development and I'm also seeing this problem, it wastes quite a lot of time and is very irritating. I'd hazard a guess that once Eclipse's class loader has loaded a class, it will check loaded classes first, find the version you built previously and never look for the newly rebuilt version.
I have not found a workaround, I suspect it would require messing about with custom class loaders inside IDL/Eclipse itself but that is speculation :/
James
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