Not knowing much about mapmodding for eu:rome but with some experience with mapmodding for eu3 I'd look into the province history files or perhaps some interface file for the answer. The history files seem more likely as they are what determines borders and the fact that the error goes away at a later date also seems to suggest they might be involved imho.
Could also just be a bug as well I suppose, I doubt the game has been tested with this many provinces before
Could also just be a bug as well I suppose, I doubt the game has been tested with this many provinces before