I just got a 19" LCD with 1280x1024 capabilites and have noticed the same problem.
So far only tested with OoT Master Quest and Super Mario 64, but both disable the "HUD" display (the stuff that is normally on screen all the time) [e.g. Mario- Can't see number of stars, lives etc. or when going to level, the text above stars is missing.]
I figure its all connected to the same object display of the video plug-in, but thats all i know.
Any help would be appriciated.