In article ,
David J. Littleboy wrote:

Wild guess follows.

Your problem may be that your software may look at the unexposed area
_between_ the frames to figure out the color corrections to apply, and if
you cut down a 645 neg, you wouldn't have those areas.

That would be my theory - either the gaps, or the area around the sprocket
holes.

To the OP - try slide film. Since it has no colour base, if this is the
cause of the problem, it should go away.