So I have been searching for quite some time to see if I could answer this question. I am no stranger to coding, or configuring Linux dists, but I haven't spent much time, if any, working on video.
I have no idea what to call it, if it's referred to as frame dropping, or what. But it seems like there is a problem with only part of the screen refreshing, leaving a disparity between the frames directly above, and directly below a horizontal line.
In Windows there doesn't seem to be this problem, the refresh rate is high enough to the point where video playback is very smooth, and there is no frame dropping (again, not sure if I'm referring to this correctly).
Here are the specs to the machine
AMD Phenom II x6 1090T - Stock Clock
8gb of ddr3 (1600mhz)
2x ATI Radeon HD5750's (1GB of DDR5 on each)
Antec 1000W PSU
100GB OCZ SSD - (For Operating Systems)
3x 1TB Samsung Spin Point HDD's
As you can see, there is not a problem with low end hardware performance, and I am running the AM64 Ubuntu 10.10.
I can't seem to get great video quality with Ubuntu, which saddens me. I've tried logical settings on most video players. Technically I can't get SMPlayer to work at all, but maybe that's just me.