I noticed that in LXDE, Knoppix, the window controls are missing entirely from the windows. Also sometimes in Unity the menu goes 'global menu' with the menu going to the top panel. If you have been playing around with either of these desktops, your window decorations settings may be out of whack. Without knowing which other desktop environment you have been playing with, it would be difficult to 'fix' your problem.
LMDE Mate 64-bit, LM17 Mate 64-bit
Debian Mate 64-bit, Xubuntu 14.10 64-bit, Ubuntu-Mate 14.04 64-bit, Antergos Xfce 64-bit, PCLinuxOS Mate 64-bit