There are still areas in Java that are not completely 100% platform independent - although if the program has been properly written, or the interpreter fully covers all eventualities, then it should be less of a problem.
Certainly I have had many experiences where a Java program written for a PC has behaved unexpectedly when run on unix or a mac. Admittedly this happens less than it use to, but it still does, and more often than not is caused by interface issues.