I think you are correct newt
I have been doing some further testing on this issue. I went backwards with C2 installs (back to 196.2) and it didn't resolve the issue with my current tilemap. If I create a new tilemap it seems to alleviate the issue. Which leads me to believe that somewhere along the line a C2 version broke / corrupted tilemaps files - and then was fixed, but left issues on past tilemap files(?) Also It seems that not only are tilemaps effected, but sprites as well. For I have been having to manually replace any image I want to update in C2.
Tilemaps :
Updating through C2 does not save. Doesn't even update texture while open.
Updating through Tiled appears to save, until next opening of file.
Manual updating via the project folder files : solves issues. (so far from what I can tell)
If I manually update Tilemap texture via project files, it works and saves.. And once that's done I am able to update inside of C2 (this is also the same method I have been using for sprites as well)
I first noticed this issue on r200 with sprites.