I did check it with what I use for a loupe (an old Minolta 50mm F2) and I could see the spots.
Here's another interesting thing about this roll. A couple of days later, I shot another roll - this was an experimental roll, so I could play with exposures, so I could work out how to process this roll. Both rolls were processed over the same weekend. While I haven't scanned this second roll, I can't as easily see the same issue. The other interesting thing about the roll with the spots is that I can't get the curl out of it, where's the second roll flattened out perfectly while drying.
As for Fungus - that could be a possibility. This roll has been in and out of the fridge on numerous occasions, but was in the wrapper until the day I loaded it.
Anyhow, proof is in the pudding. Attached are two images. Image 1 is the full negative, image 2 is a 1:1 crop of the 1600 pix/inch scan, from just above the windscreen, clearly showing the dots.