Nothing obvious is coming to mind on your problem. Not getting a map.rwm when you were before and all you've done is add region is rather strange. Have you done anything different on the 3rd region in terms of the faction or rebel type it uses in descr_regions, or for the faction creator in descr_strat??

It sounds like you've investigated most possible causes, if all else fails zip the campaign folder together with the ..._regions_and_settlements.txt file from data/text and upload it somewhere so other people can see if they can spot problem.