I was about to [romote my pawn to a queen by capturing an enemy piece when the board just would not accept my move. This has happened to me on several occassions.  I baffled by this.  I lost on time because the board won't accept my move. 

Below is my game for you to see:

Event "Live Chess"]
[Site "Chess.com"]
[Date "2012.11.06"]
[White "scrofulus"]
[Black "Fried_Gohan"]
[Result "1-0"]
[WhiteElo "1465"]
[BlackElo "1382"]
[TimeControl "5|2"]
[Termination "scrofulus won on time"]

1.e4 e5 2.f4 d5 3.exd5 exf4 4.c4 Qh4+ 5.g3 fxg3 6.Nf3 g2+ 7.Nxh4 1-0

I don't see any reason why this would have happened, i.e. you weren't in check. However glitches like this occur sometimes, so I would probably contact chess.com and see what they say.