Ok, did some more checking in the game with that Julii campagin. I noticed that under the population growth bonuses there was only a +0.5 bonus for having a land clearance. I sent my armies strait north and took Patavium on turn 2. There was no Land Clearance built there yet and it has NO bonuses to growth or farming income AT ALL.

So, all my cities are receiving no base farming values at all, only those from improving the farmlands, so every city is effectively the same.

I assumed there was something wrong with descr_regions, so I checked it. In the Imperial Campaign folder the file is missing, however the trade goods are still present on the map. In The Mundus Magnus and Sons of Mars folders the file is still there, and everything seems to be listed properly.

I'll post more after I find anything else out.