Don't know that you should have that much problem with it. Maybe I'm the only one who's had similar issues to yours?
I have had to reboot my 2 yr old machine every other time I download from the camera. No biggy, I have some patience but it's a hassle obviously.
I also believe movie maker doesn't work well with even reformatted mov files. It works if you jack with it and it's easy to navigate and so I deal with it. I have the bundled Cyber Director also and it crashes when I import the drift files to it. So WMM it is, even with it's faults.
In short, reboot your machine before you edit and see if that helps at all.