On the one hand, I know the mkvs are because the original sources are nice high-quality HD level things, so yay. On the other hand, omg mkv suuuuuucckks. Everything hates it! Maybe newer versions of Premiere can cope with it, but mine won't even recognize the file type as existing. And mpeg streamclip won't recognize it, either. ugh ugh ugh.

FWIW, when I brought the muxed file into mpeg streamclip, it still choked on it, even using the most recent beta release. (Which is what I use to strip audio out of things.) But going back to My MP4Box GUI and queueing up just the video files worked fine; they import into Premiere without a hitch, and seem easy to work with.