I noticed a very high CPU usage when using gl output in mplayer, and other opengl apps for that matter, which I think sometimes causes small pauses. Strange flickering when in fullscreen mode is also present when I try to bring up gmplayer menu.
I've tried with nopat option but the cpu usage is still very high, depending on the video size.
I'm beginning to remember problems I had with drivers when I had 9550.
EDIT: I've tried 8.7 and it also has high cpu usage, can somebody tell me if this is normal behaviour? When I had nvidia card I used x11 output (now it doesn't scale in fullscreen which renders it useless) so I have no comparision.
gl output has always high cpu usage... you should use xv instead...