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Would it have something to do with garbage collection?Probably it would have something to do with pointer bugs in your JNI code or even in the library you use.
A SIGSEGV occurs when the OS sees that the application is doing something it shouldn't. The fact that it runs on a different OS without problem would be irrelevant in the case of a pointer bug, because the execution path is different - thus the impact of the bug would be different.
That said because you are running 64 bits there is a remote chance the cause could be due to a bug in the VM. There is a thread in the JNI forum that refers to a specific option which helps with some cases. Whether it applies with you would require that you track down the message.