I faced the same problem with the Emirate of Sicily. I found the solution after a long search. I have to modify the startpos.esf file by using the pack file manager. I will send you a link to explain the steps and then let me know if you do.

To change buildings: Compressed Data/ Campaign Env / Campagin Model / World / Region Manager / Region # / Region Slot Manager. Region 135 is Brundisium, Region 136 is Syracuse. You can change the data for each building slot as you like - major is for capital buildings, minor is for non-capital buildings. You have to be careful to match the slot type with the building, if there's one there, or else it'll crash. But it's pretty easy to figure out.