I've also come across this bug and investigating further, I found the problem is with the sun-java6-* packages, not with gpsprune per-se.
When the system is configured to use openjdk by default, gpsprune works fine. The issue with Sun Java is that it does not find libraries located in the /usr/lib/jni directory. This was discussed in this thread: http://lists.debian.org/debian-java/2010/09/msg00009.html Failing a system-wide solution to the Sun Java problem, a workaround is to patch the gpsprune startup script to add the following line: export LD_LIBRARY_PATH=/usr/lib/jni
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