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Pete,
Have you tried doing a really big stretch on a couple of the raw subs to see if you can see any traces of the dark tracks? Perhaps try inverting the stretched image as well. If there are no traces there, I'd try the same on some calibrated subs to see if the calibration process is causing the problem. Next thing I would try is a simple average integration without any rejection, maybe even without normalization. Just play around and look for where they are coming from. Having found the source you might be able to do something about it.
My guess is that the tracks are in the raw data but very faint.
Cheers,
Rick.
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