The reprap software comes with rxtx and java3d binaries needed for 32bit architectures so getting the reprap software working on amd64 either means installing 32bit version of java or installing native 64bit versions of the libraries. I preferred the latter option here is how I did it.
For java3d its a simple these can simply be installed using
sudo apt-get install libjava3d-jni
For rxtx you can download binaries for the latest pre release version here expand the zip using
copy the 64 bit binary to /usr/lib
sudo cp rxtx-2.2pre2-bins/x86_64-unknown-linux-gnu/librxtxSerial.so /usr/lib
Now all that has to be done is to soft link these libs to where the reprap software expects them to be
cd reprap-mendel-20100105 rm lib*.so ln -s /usr/lib/jni/libj3dcore-ogl.so ln -s /usr/lib/librxtxSerial.so