Hi Kaidonni - it's not a problem unique to BKB's mod, others have come a cropper with it as well. The root of the issue is the way MTW defines its province borders, as it is this which determines where the port "acts", the position of the port on the map is purely cosmetic (if you want to place the port for Rome in the middle of Volga-Bulgaria on the map you can do it, but it will still "act" in the Tyrrhenean Sea...)

The secret is that the first sea region defined as a neighbour in the SetNeighbour lines in the startpos file will be the one where the port "acts". The good news is that it's easy to fix in your startpos file, simply re-arrange the order of the sea regions for the affected provinces