I've run into a little snag regarding a desktop application I developed. (http : //bioinfoserver.rsbs.anu.edu.au/programs/clans/).

The problem is not with the program but with the way java seems to handle off-screen desktops. I am running linux with multiple desktops. As soon as I switch another desktop to "active", the program stops. As soon as I switch back to the desktop in which the program is active, it resumes. I can plaster over the program with other windows and the problem does not appear, it's just a switch of one active desktop to the next that seems to "pause" the program.

What I would "like" it to do is simply continue running even when on an off-screen desktop.

This used to work fine with java 1.5 but has stopped working in 1.6. Is there any way to tell the program not to worry and just continue executing as though it were on an in-focus desktop?