I loaded your .scn file. Comparing your pbedit.log file with the one I generate here, at the tail ends they show:
BONAtheoryBug4.JPG (Size: 484 KB / Downloads: 4)
To the left, your pbedit.log. To the right, mine.
I can't explain the extra several dozen lines at the end of your pbedit.log file, missing from mine. Can you?
To focus on just one example, in your setup, you have
...
opening American/Units_100/Col Roysdon.bmp for reading
...
When I open your .scn file, there is no attempted American/Units_100/Col Roysdon.bmp file read (hence that log entry is missing here).
And so on.
Evidently, we are not on the same page, game data-wise.