I did a search for "Plan 9" in this forum, found two posts which aren't related to this. One was for the .divx the other was for iPod. So, if this is a solved problem, very sorry.
I've downloaded the fullsize videos (two part, mpegs) for Plan 9. Part 1 plays okay, part 2 doesn't. I've tried to use MKVMerge to stitch the files together and I get "Invalid MP3 Header" for part 2. Which is odd since part 1 is made of MP1 and MP2. Tried using MKVToolnix 2.4, 2.9 and the newest build via ports.
Quicktime Pro won't open it, Photoshop CS4 won't open it, Double Twist won't open it. VLC will open it, but the video is scrambled for the first dozen frames or so. Plex shows a similar amount of video missing. Both VLC and Plex use FFMPEG codecs.
My MD5 checksums match, so it's not a bad download:
blaine% openssl md5 Plan9FromOuterSpace_Part_02.mpg
blaine% openssl md5 Plan9FromOuterSpace_Part_01.mpg
Computer specs are OS X, latest updates of Perin and FFMPEG.
My end goal is to get the higher quality video (the DIVX plays fine but I'd rather have the higher res one) and strip in the original soundtrack as an alternate commentary in an MKV - like I do with all my Rifftrax. I really don't want to re-encode, just remux the video.