I just started trying out Snagit 11 on Windows. It now records screencasts in .mp4 instead of .avi. I thought this would be great but there's a problem. I typically record a screencast and then open it in QuickTime Pro 7.x and edit out the bits I don't want. When I'm done I export to .mp4. When I tried to do this with the mp4 that Snagit11 created, deleting a few seconds of video would actually delete a couple of minutes. I tried it multiple times and it was very repeatable. It got the starting point of the cut correct but it didn't get the stopping point even close. I'm not sure if this is a problem on the Snagit11 encoding side or on the QT pro side. I've never tried to edit an MP4 before. I don't see why this wouldn't be possible and I can see how I might lose some precision in adjusting playheads on an already compressed format but to miss by a couple of minutes seems a wee bit extreme. Are there any tricks I need to know to edit a video in QTPro that is already in mp4 format?
I think the short answer (one you may have already found) is no! I'm in a similar situation: I write music to picture and used to receive clips as .movs. I could then add final audio myself for showreel/web purposes. Now those clips arrive as mp4 and are useless and unchangeable. I can merge files in QT pro for viewing, but no saves are allowed.
Editing software usually prefers 'linear' formats (aiff or wav for audio, .mov or similar for vids) whereas mp4 is heavily compressed and 'lossy'. Also, the key frame rate is very poor (300 I think) so that might explain some of your edit problems. The only workaround I can find is to open in QT and re-export, but the results are pretty ugly! Saving to mp4 for final product? Why not - it looks pretty and the file sizes are good. Working with mp4 in the edit? Hell no :)