I get this too with both sonata and guimup. In both cases icon is
actually in systray but are badly scaled into 1x1 pixel size. You can
see this with other items shifting a little in tray, or as is case with
guimup, a one colored pixel appearing in tray. So this is most likely
same scaling issue th
Would like to point out that this isn't limited to 1280x1024 resolution.
Had this happened few times with Quake4/ET:QW on my native 1920x1200,
although it doesn't happen always and most of the time I can play on
fullscreen just fine.
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SDL applications auto-leave fullscreen if set to native 1280
I got the same thing with ET: Quake Wars on Xubuntu 8.04. It seems to be
related on other windows stealing focus from fullscreen app. In my case
this was fixed by disabling popup notifications from sonata.
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Compiz causes OpenGL fullscreen games to eventually go windowed.
https://bugs.launchpad.