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.
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.