First, check that the "Use high-quality video setting when available" option is checked in Quicktime preferences. For some reason it is unchecked by default.
If that doesn't help post more info about the files. Most importantly, where are they coming from? What app are you exporting these files from? Are the files being created on the same computer that you are experiencing the problem with AE import? How do the videos look when you open them in Quicktime player?