However, noticed it's made some terrain darker. Note the wheat in background. Is there some sort of filter being applied in the new game or ini settings?
Yeah that looks like the same issue we ran into. I'm not sure what is causing it, but it did the same for the new Waterloo sprites. It makes them darker, and less transparent--the alpha channels have hard jagged edges, instead of the smooth look you see in the game now. Just something we ran out of time to troubleshoot much, and decided it was best to just leave them unpacked.
However now that you can re-create it on non-Waterloo map, hopefully that will help us narrow down the cause.