Since it's been reported, I've been trying to fix this bug about flickering Mame windows:
https://bugs.launchpad.net/ubuntu/+source/mame/+bug/994508
but it seems it's not related to Ubuntu-specific stuff (i.e. Unity).

After a lot of testing, I'm currently blaming OpenGL, as the bug only occurs when all the following options are in use:

-video opengl
-window
-maximize (this is not mandatory, the bug seldom raises on non-maximized windows too)

marcello also reported that compiling mame with the -O2 switch introduced the bug on Debian.

I've already tried different WM (Gnome 3 and IceVM); disabling OpenGL (-video soft) removes the bug; I've tested Mame with an NVidia card (both stable and beta drivers) and an old ATI one.

Weird enough, once resized to be completely displayed within the screen, the window shows properly.

Anyone else is experiencing the bug?

Odd. Normally I'd suspect the fairly well known Linux issue that "OpenGL app + compositing WM = horror", but as far as I know a lot of those problems have been solved (I'm not seeing them with KDE 4.8 on F17; I'll try GNOME 3 later).