Only thing I can think of is, look in your rtw.exe folder level at the corrected_regions.tga (this is always generated regardless of wether corrections are needed).

If this shows that the port pixel has been lost, it is due to the fact that your map_heights.tga doesn't quite align, and that has priority for the coastline.

Also check that port pixel is pure white ie. RGB 255, 255, 255.