I don't have a solution, but are you sure this isn't a problem with the scanner?
I used to have a Flextight and found on dark even surfaces (like your sky) I would see stripes in the direction of the scan. It was due to an unevenness in the bulb (this was a new scanner, so not due to aging). I eventually got new bulbs to fix it.
If you're unsure reverse the neg and rescan it and see if the most prominent stripes flip to the other side of the image.