Last time this happened to me I was working with an Uncompressed 10-bit SD codec on a NASCAR spot. I'd make edits in the Viewer and cut them into the timeline, and the minute a render happens, the whole clip shifts wildly, with no consistency (ie. a shift of 25 whole seconds on one clip, and a shift of 10 seconds on another).
If I remember correctly, the assistant editor mis-set the Capture settings so that the input signal was coming through SDI but the Device Control was FireWire (!), or something like that. (Don't quote me on those settings -- this was months ago). I ended up offlining in DV codec with new captured clips, then recapturing only selects using AJA Kona 2 525 10-bit 29.97fps presets, and then manually re-conforming the edits. Didn't even use Media Manager because the timecodes were all over the place and we didn't have the time to keep implementing uncertain solutions.
I have no idea if your situation's the same, but you should try recapturing one problematic clip and use an HDCam setting. See if the problem goes away.
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