You mentioned frame rate and format: do you think the XDCAM-EX 1080 24p might have something to do with problem?
I’ve also read that using a still frame at the beginning of a sequence can create problems. In the two examples I described above, however, only one of the sequences had a title (format: still) at the head of the sequence; in the other sequence where titles went awry during m2v. transcoding, the title was an end credit.