When you say work, do you mean they don't play, the larger files?
For h.264, they must be transport streams. We won't have .mp4 and .mov support until a little later this year.
For mpeg2, any .vob or .mpg file should work, mpeg1 system streams, and mpeg2 program stream and transport streams.
Please send me an email at <!-- e --><a href="mailto:support@brightsign.biz">support@brightsign.biz</a><!-- e -->. I'll forward ftp directions so you can upload a couple sample clips that aren't playing.