This situation looks very similar to the following thread and a solution is posted there:
EDIT: Scratch that. Your situation sounds a little different, sorry. But if you are familiar with text editors, you could compare two .MLT files side-by-side and see what’s different about them. By any chance, is there a Rotate and Scale filter applied to the track head of the track you’re dropping videos onto? Any filters on the V1/V2/V3/etc track heads will apply to all clips on the track.