When you start a new patrol there are no rendered ships and the SH3 engine has to render them from placeholders in the _SCR layer, so there is no harbour bug.
If you then save the game in the harbour and load
from the savegame, the ships have already been rendered once and SH3 'remembers' them as rendered ships (not placeholders) therefore you get the harbour bug.
The issue is not with the _SCR file, it's with where and when you save your game, and bear in mind that ships are rendered from the SCR layer in the last few seconds before the game starts (about 95% through the load bar). RND is about 50% of the way through the load bar. It's easy enough to test - script a standalone ship (e.g. one of VonDos') into the SCR layer then
disable the ship in JSGME. CTD @ 95-100% of load bar. Script into RND and CTD around the 50-60% mark.
I'm also fairly sure that there are a finite number of rendered ships that a savegame can cope with:
A few rendered ships - no problem, waypoints saved (try it next time you see a single merchant)
More rendered ships - SH3 will remember the ships but ditch the waypoints (harbour bug).
Too many rendered ships - CTD (near large convoys etc.)
Unfortunately the number of ships the savegame system can cope with seems to be computer dependent. Those with top of the range computers will suffer fewer problems than those (like me) with old ones.
We seem to have derailed TGW's thread so apologies to TDW (and the rest of you!).
@LGN1 - if you'd like to continue this we should start our own thread for it.