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The vertical bar is in the left and it's much wider than and unrelated to the Unity side bar. It's as if the desktop area does not include a left vertical bar, but only for maximized windows: (parts of) other, unmaximized, windows can access (occupy) that area and are indeed thus visible (in that area) when the window is maximized. I switched to metacity and I got the same problem. I also restarted Unity, without logging out and back in.

I need to know the reason. I know a reboot will fix it.

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This line in a script I tested is the culprit: xprop -id <any window> -f _NET_WM_STRUT_PARTIAL 32c -set _NET_WM_STRUT_PARTIAL '200, 0, 0, 0, 0, 200, 0, 0, 0, 0, 0, 0'. Replacing 200 with 0 solved the problem. (What would be a general way to undo all such xprop changes anyway?)

Somebody please explain why it affects all windows even though I used it only for one specific window. Some explanation as to what this line was supposed to do wouldn't be bad. If there is no answer in a while, I'll "accept" mine.

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