On my home machine (iMac 10.6.7, iTunes 10.3.1, Perian 1.2.2) these videos play fine in iTunes and everywhere else.
On the "music videos" Mac Mini at DNA Pizza, (different hardware, but same versions of OS and all software) in iTunes, some videos play solid black video (though audio is fine). But they play fine in both versions of QT Player.
If I do "Get Info" on the video in iTunes when it is not playing, it says "Video Dimensions: 640x480". If I do "Get Info" while it is playing black, it says "0x0".
Fails the same in either full-screen or windowed mode.
For these videos, iTunes also can't generate a cover-flow preview image.
Get Info in QT Player shows a completely normal looking set of sizes and codecs: H.264 (Perian), 640 x 480, Millions; AAC, Stereo, 44.100 kHz; FPS 29.96; Data Size 22.39 MB; Data rate: 914.34 kbits/s.
The files were encoded with either Handbrake or MPEG Streamclip. Identical files on both machines.
I am completely at a loss at to how iTunes could be having a problem with these files when QT Player does not, or why it would be different on the two machines, or what I can do to work around it.