Hi Derek, thanks for the quick and thorough reply. Changing the ffdshow settings worked for Divx and H.264 which use the ffdshow decoder. In fact it was unchecking the YV12 option that made it work. However, the WMV videos still had the problem. I also tried encoding with pp=fd (which I assume uses ffmpeg instead of mencoder). That did not have any effect, as in, if I checked the YV12 box the yellow ghosting came back. I also tried encoding using the WMV (no resize) preset, which had the scale:-2 option like you mentioned above. This did fix it. However, i found that the scaled version actually looked better because the unscaled video was very pixelated (everything looked like little squares), even though it was higher resolution. Because of that and the file size, I will probably stick to the scaled version. On another note, contrary to what I've read, fast forward/rewind and skipping both work on the WMVs, so it would be nice to have the option to use that format.
As far as the skipping, it seemed to be only encoded versions of that particular DV-RMS file that skipped a bit during the beginning, though the original DV-RMS file did not. So it's not a big problem. Is it possible that there are bad edits in that video that aren't getting de-interlaced properly in the encoding?
Now the next question: why is my video not converting YUV->RGB correctly? It is an MSI NX8500GT-TD256E, which I just got a few months ago. I confirmed that it was the card by switching to the internal Intel 950 chipset graphics, which worked fine with the WMV file. I even updated the NVIDIA drivers to the latest version and it did not fix it. It seems like such a current graphics card shouldn't have problems like this. Any ideas?