OK after much testing I found the problem.
I had unchecked 'Track selected game list and game' from GUI...Options...Gamelists. Putting the checkmark back fixes the problem. When I put the check back in (on the all games list screen) I got an error, here it is from the log:
2009/04/24 11:44:54.53 Error: Object Class: TTimer, Object Function: DisplayMarquee, Exception Class: EListError, Exception Message: List index out of bounds (22)
I closed out of MaLa and went back in, since then no errors and no issues with the gamelist.