I suspect the eclipse framework rendering engine has an off by 1 error.
Sometimes when using a Notes application (frameset + view) like Mail, the Mouse clicks appear about 1/2 inch above where the mouse cursor is pointing in the view or any navigation (including the search dialog) is above where the pointer is located. And sometimes it is accompanied by a UI glitch that hides the view’s action bar. The distance that the click is off appears to be the same size as the “missing” action bar, or perhaps the search bar. This can be fixed (work around) by completely closing the application OR by expanding the side pane! When chaning the side panel from hidden, to icon to full size, it will fix the view, but not the navigation frame (far right). The navigation frame can be fixed by docking the Open menu.
Any view in the application exibits the same behavior once the symptoms start. They usually start after switching application tabs. Unfortunately, I have not been able to reliably reproduce the issue. It happens on different applications at different times. But it has happened every day (sometimes twice) since installing 8.5 beta2. It happens on different applications (mail, document library, etc).
Platform specifics: SUSE 10 + community patches up to 11, NVidia, Gnome (and KDE3&4) w/ Compiz.