mplayer2 downloaded and installed a new codec to read the .wmv files, which certainly helped. But in this program I get a different sync problem, where the visuals appear as if in fast-forward for a few ms before settling, leaving the audio lagging behind.
WMP 11 doesn't seem problematic anymore though (when playing them in standalone mode), but there is still a slight inconsistency when running DirectRT - I can run the same video stimulus three times and one (it seems to change each time as to which one) will jump at the start (leaving visuals slightly behind). I've minimised it by setting the trial interval to 3000, but it still happens.