Since these videos are for your own use, why not try
Quicktime, PhotoJPEG(60-75% quality)
, uncompresed audio(or just export the audio as a WAV separately and keep audio out of the resulting video file).
MPEG Streamclip should have little trouble producing those.
Also a decent option are
MKV containers, which can be produced with the software
Handbrake, also free. The sound can be decodec in to almost any format, except for uncompressed audio.
In film work I might use the Quicktime audio as a guide track, but I always have it as separate audio so it's available on its own track, which is what Protools offers to do for you anyway.
Now of course, there may be something wrong with your system. May be. To test for that we should try other video files.
The MP4 files you can download off Youtube (with a Firefox extension like DownloadHelper or a dedicated tool) work very well in Reaper.
Meanwhile I'll prepare a small clip for you to test as well.