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