Mukund,
IIRC the JBuilder feature of creating an EXE is not a real EXE, it requires certain settings of the VM on the Windows machine you are going to run it. AFAIK the only true EXE creator program out there (I think there are 3 major ones) is the JET Compiler. I’ve used it on a few occasions and its really good at what it does, but not free, and I figure you might want something free.
If your application runs using SWT, you could use GCJ to compile a binary, but it would be via a nice plugin 🙁