http://forum.processing.org/topic/ubuntu-is-logging-me-out-when-i-m-trying-to-run-program-in-processing

and click the "I too have this question" button there.  Looks like there's no answer yet, but there are some things you can try. Also, here's a search for ubuntu-related threads.  Not sure any of these will help, but here you go:

http://forum.processing.org/search/ubuntu

I may try to put together a Ubuntu-problems FAQ soon.   Meanwhile, put any future posts on this topic in the thread I linked above.  Besides the benefit of keeping all the discussion in one place, a bigger thread will get more attention, which means a better chance of finding and fixing the problem.  Good luck.