It also mentioned matroska.
Right, but it was referring specifically to high-def content contained in a MKV file wrapper causing problems. XviD/DivX content in a MKV file works fine in FFDSHOW.
The problem was that apparently FFDSHOW is loading even when it isn't needed when it thinks it can decode the file. Unfortunately, FFDSHOW can't properly handle the h264/mpeg-2 high-def content and chokes, causing the stuttering.