The starting locations are in the flotilla.cfg file. It's in the \silent hunter III\data\cfg map. You can just edit it with wordpad.
It's a file with a huge amount of text, so just press ctrl-f and enter the name of the port your flotilla is currently based.
A couple of lines below the name of your flotilla's port you'll find these lines:
DeparturePointLong0_0=1218360.000000
DeparturePointLat0_0=6521927.000000
(just an example, these are from Kiel)
You can edit those figures, but I have no idea how coördinates work exactly, so you'll have to ask someone else about that... Hope this helps a bit.
btw, as far as I can tell, this problem shouldn't be caused by any of the mods you're running. But if you don't mind me asking; why are you running merged campaign?
It causes sh3 to take a huge time loading; because you're loading all region's which is only necessary when you're transiting from the Atlantic to the Indian Ocean..