All Smoothcammed Clips Interlaced Backward?

Compressing a bunch of 1080i footage down to DVD, I find that all Smoothcammed clips appear to be interlaced backward! That even though the non-smoothcammed clips seem fine. Anybody seen anything like that before?
This all comes back to earlier discussions, notably
http://discussions.apple.com/thread.jspa?threadID=2270427&tstart=0
it sounds like the only way to keep Smoothcammed sequences from becoming spontaneously unrendered is to re-export them as QT movies, and import them back in. I discovered that they seem to always be interlaced backward when I export them. When I import them back in, they seem to often get contorted further (possibly scanlines going from 0 1 2 3 to something like 3 1 2 0, but I'm not sure).

I think I understand now what's really going on: It's not really getting interlaced backward. It's just that, as Smoothcam makes adjustments for shake, it has no choice but to adjust the two fields of the frame separately. When it does so, we get flicker galore.
I wish I had a 1080p camera! Maybe for those sorts of shots, I should shoot in ... well, whatever is the largest frame size my cameras can shoot in, non-interlaced.

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I am using final cut express 4. It seems that any clip over a certain length, say 5 min, does not fully transfer! All shorter clips are perfectly fine. Is there some reason why longer clips are not fully transferred? (a half blue circle shows up on the transfer list, indicating that the clip was not fully transferred. When I check in the capture scratch folder, sure enough the whole clip is not there!
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Thanks for the reply. I'll try to answer all the questions (I am a relative novice). Your help is appreciated.
By the way, the other reply I received suggested the following:
In Final Cut Express>System Settings>Scratch Discs make sure the Limit Capture/Export File Segement Size To: is not checked.
I did this and it was already unchecked. So this is not the answer...
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ANSWERS
how you are ingesting the files
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the format of the source footage
digital via ext flash memory. Frame size :1929X1080 / 25fps
what camera shot the footage
SONY HXR NX5
how you are connecting to the computer
from flash memory directly via usb
what version of FCE you are using
4
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10.6.8
what model Mac
macbook Pro intel Core i7
what drive you are using for Capture Scratch
3TB external drive (plenty of room left)

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All Smoothcammed Clips Interlaced Backward?

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