If editing directly in MOV causes problems, you might want to convert your files into another format. This, of course, may result in loss of quality.
While I haven't used an up-to-date converter myself for quite some time now, there are various good ones available as freeware. Check, e.g., here for mov to avi converters:
Download mov zu avi freeware
I seem to remember a freeware tool called Super(C) which I used successfully to convert audio files. It also converts video formats.