i've only noticed a minor issue.
the seek bar on mplayer os x extended under 10.6 Snow Leopard blinks while the file is playing. you can't notice it until you actually reach about 5% of the file but the longer you seek, the more you will notice it.
Not a major problem, just a cosmetic one i guess
EDIT1: ok another issue.
I use mplayer with the separate window setting and as such, the mplayer window displayed has a strange bug:
there are 2 apple menus as you can see on the image. This bug doesn't make any strange behavior but it's another cosmetic bug, and i think the cause of it, is the underground changes Apple made to the Service menu.