Yeah I've had a few video podcasts from itunes and even some videos from apple.com not play. I think it has something to do with the scale of the video that has to be with in spec, so does the audio encoding.
Here is the video spec list from apple.com:
Video
Video formats supported: H.264 video, up to 1.5 Mbps, 640 by 480 pixels, 30 frames per second, Low-Complexity version of the H.264 Baseline Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; H.264 video, up to 768 Kbps, 320 by 240 pixels, 30 frames per second, Baseline Profile up to Level 1.3 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; MPEG-4 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Simple Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats
15" SR 2.4 MBP Mac OS X (10.4.10)