I am using Steam with the kingdom campaigns and proceeded as follows:

Used a mod (Clouds over Europe) where the max port (regular, not castle) and wharf resulted in three sea export lines in Murcia (moors).
I then gave this settlement the base port and base wharf which resulted in 1 line
base port and next level wharf - 1 line
base port, no wharf, 1 trade fleet bonus for port - 1 line
base port, no wharf, 2 trade fleet bonus for port - 1 line
next level port, no wharf, no trade fleet - 2 lines

It would seem that the port levels are hard coded where number of trade fleets are concerned, 3 fleets for the first 3 levels no change in 4th level, and that the trade_fleet capability has got no effect whatsoever.

Pretty sure at some stage it worked as it should, maybe when the executable got merged it got messed up? Or with the disk version?