HT3775 AVI's appear green once converted from AVI to Quicktime

Dear Apple Tzar's,
Having recently become as Mac user, I recently purchased iSkySoft Video convertor so that I could convert my library of avi movies (that I use for medical teaching) into Quicktime.
Weirdly some of the movies I convert work beautifully, while others convert so that all can be seen is a large green blanket of nothingness.
Any thoughts ? many thanks for your assistance,
Many thanks,
Beth

TSM:
Thanks for the reply. I'd be "LOST" without you!
Anyway, the camera only came with a Windows disk. Per the manufacturer, it doesn't need mac drivers, and the windows drivers are only for the web cam function (which i don't use.)
The camera is formatted under FAT32 (Windows) format. I couldn't run permissions repair. I did do a repair disk under disk utility. Still having the issues.
I tried iMovie. I can import the avi file from the camera, and it works!!!!
So it would appear that there's a bad codec in QT/Perian/VLC?

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