http://dvdripping-guid.berlios.de/forum/viewtopic.php?t=16&sid=35755ea831ffeb094b921e95c2ba5d13
If you get wrong colours when transcoding some files, remove the -V option from transcode options. That will solve all problems.
The -V option uses the YV12/I420 as internal video codec which is much faster encoding, but it has problems with some files.
I mean some weird red shadows, and there are on the left and right mirroreffects of the film. To know you are having this problem, transcode will give you this warning during transcoding:
[video_trans.c] warning: odd clip parameter invalid for Y'CbCr processing mode