Just encountered a frustrating problem trying to use yEd and Visual Paradigm for UML over Ubuntu. I am using a dual screen configuration. When either of these applications (and I am sure many other Java apps) are fullscreen, clicking the menu does not seem to work. Drag’n’drop of shapes seems to be imprecise, in fact it seems like the mouse has a sort of “offset” between the cursor and the actual mouse position.
This is solved by not having the window in fullscreen.
Here is another description of said problem: http://yed.yworks.com/support/qa/438/java-7-on-ubuntu-menu-mouse-error