The icons don't actually have a grey background. Java has a bug that affects X (see http://bugs.sun.com/bugdatabase/view_bu ... id=6453521
When I did some searching I came across this: https://github.com/taksan/native-tray-adapter
which looks promising at least for systems using GTK. The nice thing is that it falls back gracefully to native AWT if GTK isn't present.
On the plus side it looks like the issue might get fixed in JDK 8 (http://answerpot.com/showthread.php?359 ... planned%3F
I won't be holding my breath.
I can't spreak for anyone else running PMS on Linux but icon-16.png is too small for the tray. On Cinnamon it gets blown up and looks horribly pixelated. I suspect that using the icon-32.png or icon-22.png would be nicer. I think that with image auto size on (which it is in BasicSystemUtils) it will scale down if it has to.