Zero timecode after capture

I'm having issues with sporadic zeroing out of timecode after capture. I have two identical systems running FCP 5.1.2 and capturing with AJA Kona 3 cards running version 3.2. All of the capture presets are identical.
The process that I've been using on both systems have been as follows:
Creating a new project
Importing an XML into the project
Batch capture from the Kona card as 1080psf 23.98 DVCPro HD
The odd thing is that one system (only one of the two) sporadically zeros out the preset captured timecode for the entire XML, thusly changing a logged clip that was set to start at 13:21:14:05 and forcing it to start at 00:00:00:00. The duration of the clip remains a constant. A usual fix for this is making the captured clips offline, trashing the FCP preferences, restarting FCP and rebatching. That usually fixes it for a few days, but inevitably returns to the same old problem. I've also tried reinstalling FCP, but that hasn’t resolved it. Does anyone have any ideas?
Thanks for your help!

So, is there a way to get FCP to display Zero-Based
timecode for an individual clip? Or to get After
Effects to read the timecode embedded with the clip?
No and no.
Have you looked at this?

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I just noticed that out of a group of about 110 JPGs I was editing tonight, about 5 of them had their Develop Settings zeroed out after I exported the files.
Examples:
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2. Another file's Fill Light went from 17 to 0 after File Export.
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4. Still another file's Black went from 1 to 0, and its Contrast went from -3 to 0.
5. Another file was rotated by .28. After exporting, the rotation in the history went from .28 to 0.
One other problem I saw with at least 2 of these files (different than the 5 above), I had created virtual pictures for these 2 and exported them as TIFFs to Photoshop CS3. After the TIFF file was updated with CS3, it automatically was reimported to LR. There is no "Import" listed in the history, nor is there any "Created Virtual Copy" in the history.
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I think I have that box checked, but I'm not sure where to find it. I seem to recall having checked something like this before, but, again, I just can't
seem to find where it is. I've checked in Preferences and do not see it, as well as other places.
Anyway, I do not export files to CS3 very often, but I know that every time I do, the edited file gets added back into the LR Catalog when I close out the file in Photoshop CS3. I typically export these files to CS3 keeping the LR adjustments.
I originally had this set of images sorted by File Name. I did that because within this set are pictures taken from 2 different cameras, with two completely different types of file names. I wanted only to work on the images from one camera at a time. While sorted by File Name, the edited file does get added to the Catalog, stacked upon the original file....so, yes, they are side by side.
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Because my other problem of settings being zeroed out appeared to be "fixed," I was hoping this problem also would be fixed. But when I tried the same procedure as last night (only with the files sorted by Capture Time instead of by File Name), the same thing happens...there is no "Import" listed in the History panel.
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As mentioned, I do not export files very often to CS3, so this problem may have always existed (not showing "Import").
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Zero timecode after capture

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