I have this too and it's fairly annoying for usability - the last line of a
gnome-terminal session disappears.
The problem seems to be unrelated to whether you've attached multiple screens
after login - maximize simply ignores a panel on a side of the monitor that
does not represent the end of the screen (i.e. another screen exists beyong the
monitor)
** Changed in: compiz (Ubuntu)
Status: New => Confirmed
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Gnome panel appears over maximized window when using multiple monitors
https://bugs.launchpad.net/bugs/298234
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