Any ideas? Not very good ones considering all the information you've given us.
Here's my stab in the dark: did you make quicktime movies? At what horizontal & vertical resolution? Self-contained?
I have MP4s (h.264) for a html website I am working on and I need to edit these in after effects to crop and change some background colours.
When I save back out howver, I update them in AE and render back out as h.264, but they dont seem to work anymore. Ive tried MP4 also, but no joy.
Use the Adobe Media Encoder to render your H264 and pick an appropriate preset for the movie size and delivery.
It's best to stream movies on the web from a video server and not from your own URL. You can embed movies from all the popular free services like YouTube and Vimeo.