I would hazard that it's some change in the patch with regards to Lanka causing flags to go up.
Cainehill: lighten up
I think the files are changed mostly to include the new units and flags and such. Indeed, if you just switch the old .exe back, the game starts up properly and displays the old version number, and doesn't show the new nations. This has been the case with earlier patches, too, despite them changing multiple files, I believe. So, at least on the surface it is enough to just back up the executable. So, I at least would be surprised if it didn't let you play older version turns by just changing the executable.