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.