FCP7 xml round trip

1080i 29.97fps pro res media and sequence settings. I am round tripping sections of TV shows that are typically about 200 shots each. Intermittently some clips render the wrong section of the source media. Sometimes it seems this happens when the source clip is very long (eg two minutes of source media for a 3 second clip) or where more than one clip shares the same source quicktime file. I don't understand why this should be the case because the timecode in the source media appears to be fine as far as I can tell.

Any ideas on what could be wrong? When I compare everything I can think of looking at between the problem clips and ones that work fine I usually cannot see any difference at all, but maybe there is something I am overlooking.

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