QUOTE
I haven't tried re-loaded all the games in the new mode (16:9, 480p enabled). Should I give it a try or am I just paranoid?
if by re-load you mean take them off your HD and put them back on, no this shouldn't change anything.
The only other thing i could think of would be to clear your cache. Its located on E:\CACHE\ and X: Y: and Z: if you delete all the contents of these folders it might help. note that you still need to have the e:\CACHE\ folder, you just delete the contents.