I am referring to inspecting the glass of the lens, front, back and internally with a magnifying glass. But, even dust within the lens might not be so obvious at first. A test that you might try sometime . . . for each frame exposed, make a duplicate exposure on the next frame with the camera inverted (upside down). If in the first frame the smudges end up in the sky as usual, and in the subsequent frame (inverted frame) they end up elsewhere; ie; 180 degrees out, then my guess is still that it's something on the glass of the lens internally or externally. I think you have already proven this by your example above, the exposure that was made in portrait (vertical). Notice how the "C" shaped smudge moved when the camera was rotated. It moved with regards to the real horizon, but stayed in the same place with regard to the camera's frame.
What sort of scanner are you using? If it is one of those that uses a CMOS sensor (so essentially a digital camera) it could be dust on the scanner sensor. My first thought was that they look like dust bunnies on a digital picture. Clean the scanner.
That's just weird. But I think Peltigera might have a handle on it. To see, check the negs with a 5X loupe, a 50mm lens from a SLR makes a good 5X loupe if you don't have one handy. Look for any sign on the negs of the smudges. If there is nothing on the negs then the problem is somewhere else in the image chain.
So I decided to closely inspect the negatives by hand and of course, I saw the smudges very clearly in the same spots as I see them as a positive when scanned. So that rules out the scanner.
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