We have a Java application that uses some C++ libraries through JNI. The application used to work just fine in Windows XP, but it does not work in Windows Vista, it just crashes
Try setting up WinDBG, and hook up a symbol server, so you can get symbols for the OS DLLs.
WinDBG
Symbols (bottom of the page)
Then run your Java app under WinDBG and trap the crash there. With any luck you should be able to find your native code in the call stack, or at least something you can recognize.