This doesn’t really answer your question I’m afraid, as without knowing all about your system and software, it’s hard to answer. But as a general rule, it’s best to convert mp4 before you use them. They are slow to work with and unreliable (as are most interframe codec media).
Interframe codecs achieve amazing compression by remembering only the changes between frames, so they are also slow to work with because to read in a certain frame they need to check back to the last keyframe. That could be several seconds before. It then reconstructs the picture by playing forwards from this last keyframe. That’s why they’re slow to work with. Examples of interframe codecs are mp4, flv On, Sorenson, h.264, MPEG2 . They also have no timecode track, so they are not always frame accurate (especially at low data rates and around cuts). And I’ve often had problems reading them in at all too.
If you can open it in a certain media player, try exporting it from that media player using an intraframe codec (note inter / intra) Intra is the opposite – each frame is compressed as an independent picture. Preferably uncompressed for working with. Quicktime Pro ($29) should open and export mp4s.
You might also consider a screen capture program.
-f.