That's weird because in my testing last night I didn't have any missed retraces as far as i can tell. The longest video I watched was about 10mins and I was watching mostly 720p side-by-side video leeched off youtube (Firefox+DownloadHelper rocks), as well as some 480p clips from 3dtv.at. My command line was usually something like:
mplayer filename.mp4 -vo x11 -vf dsize=1280x720,scale=2048:768
Pentium D 3.0Ghz (2xPentium 4 HT in one package, 800mhz FSB)
2GB DDR2 666
Geforce 7900GTX 512MB (Not using hardware accelaration because -vo is set to X11)
Not quite sure if the mplayer I used was the stock one that comes with Ubuntu or the version I built from SVN a few months ago, I will have to check when I get home. Some things to think about:
Does your machine hit 100% CPU when it drops frames?
Does the CPU load causing frame drops come from userland or the kernel?
How fast is your machine?
Does mplayer drop frames playing the same video without genlock enabled?
What timer options do you have in your kernel? Hight precision event timers? Tickless/Dynamic Kernel?