You guys are skirting around the problem, which I've brought up several times..... alt keys should not be used in your setup, period, end of story. Not all games support them (mainly because it's a bad idea to do so). And alt plus ctrl or enter ect causes windows to go crazy.
Remove alt and adjust everything accordingly. It's a lot of work, but you'll be better off in the long run.
On an O.T. side-note..... For those of you who wonder "Well then why do the mame devs use that layout?"
Well when mame was first being developed doom and early fps shooters were all the rage. They copied that default layout. They also copied the menu system keys for the record. The thing is those games ran in dos mode, so you could get away with using the alt key (no windows to confuse). Unfortunately this ill-concieved tradition still lives.
You can stop the madness, friends don't let friends use special keys in their layout. Only you can prevent badly planned key setups.