FCP renders different part of footage

I see that other people have had this prob in the past but I don't see any solutions... Everything plays fine in my timeline, but when timeline is rendered or exported, FCP substitutes a different part of the footage, so I end up with all these random shots in my piece.
Also, the thumbnail for the clip in the timeline displays a different image than the clip I've selected.
And there is a lot of black at the end of my captured clip (as though audio and video are not in sync).
This all started when I upgraded to FCP 6.
Thanks anyone who can help!

Sure, thanks. It's happened in a variety of projects, with different types of footage, but I'll give you specs on the project I'm working on now as an example.
Footage is 720x480 29.97 NTSC captured from DVCAM (this footage worked brilliantly in another project last year).
Sequence settings:
720x480
NTSC 3:2
CCIR 601
compressor DV/DVCPRO NTSC
OSX 10.5.6
FCP 6.0.5
QT 7.6
We capture footage using a router and AJA Kona LH but have also experienced same prob with footage captured via Firewire.

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