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Is it possible for you to try another desktop environment just to see if that works better?
JRockit Mission Control 4.1.0 does not officially support Ubuntu, but of course we want it to work.
We'll probably try to support Ubuntu with our coming Java Mission Control versions, not sure which desktop environments we'll support.
We're based on SWT from Eclipse, could be that it's not working correctly with xfce. Apparently there are other problems: http://forum.xfce.org/viewtopic.php?id=3473
So, i told you I'm running on xfce. But I'm using "gnome" like desktop manager. My mistake.
But this isn't probably fully working gnome. I'm not satisfied with unity so i installed some packages to make my system able to use gnome classic instead of unity.
I have no problem with scrolling on xubuntu.
You can try find solution for it ;-)