Apologies for bringing this back months later, I'm due a new computer, and an AMD graphics card is a possibility, so I'm quite invested in the outcome of your experiments :)
Anyway, I was just having a look at the MOS files you discussed above - and I was opening them in a hex editor to read which files they referred to (I can't get the Mos editor to run).
I may be completely barking up the wrong tree, but it looks like the river files, and possibly the town files are referring to files which don't seem to exist anywhere.
RiverHoriz.mos (and other river ones) refer to a RiverHoriz1_watermask.dds
Most of the river files refer to a non-existent "watermask.dds" - i.e. RiverSourceLeft_watermask.dds
CitySummer.mos refers to a Village04_winter.dds
134summerTownCentre.mos refers to a eneric_1_outline.dds
It's possible, in the Mos editor, it would become apparent that these were just leftover references from when the graphics were made and aren't actually used and don't matter etc, but I thought it was worth mentioning just in case.
As far as I can tell, none of those files exist. Is it possible Nvidia cards are showing a missing texture as invisible, and AMD cards are showing a missing texture as a black square?