[java] JNI and Linux

I have a game that is cross-platform in C++. The game works perfectly on Linux and Windows. I''m trying to port my Editor (which uses Java and JNI to interface with the game) to Linux and it''s giving me all kinds of nasty problems. Has anyone done something like this before? Is there an older version of Java which works better than 1.4.2? Or should I post in the Linux forum? Thanks! Tom