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A few searches in the Bug lists reveal that this problem has been around for a long time, also that there have been several fixes. But the problem persists, at least here on Linux-GTK-AMD64 and, as long as I can remember, for versions since 3.2.2 and also some of the 3.3 branches which I tried over the last months. On restart of Eclipse or on workspace refresh (i.e. through opening a project) all visible columns in the tasks and problems views get their width increased by 3 pixels (this amount is probably connected to some settings of my window manager, but that's only my assumption) causing a horizontal scroll bar to appear (given that before it, the total width of the view was utilized optimally) and, after several restarts/refreshes, moving the rightmost column out of the visible area. The problem also seems to be related to the Linux environment, since I cannot remember having had this bug on Windows XP, about two years ago before I switched over to Linux. I considered writing myself a small program (executed beforce starting Eclipse) which just overwrites the affected parts of the workspace XML configuration files to get rid of this annoyance, but that won't fix the problem occuring on a workspace refresh.
Which window manager are you using?
*** This bug has been marked as a duplicate of bug 235018 ***