I'm thinking that lurker "fixed" the issue, but I'm not sure. I think Webster did similar in GFO, but I don't remember for certain. I'm also pretty sure that ducimus noodled with Jap_HarborTraffic also... But don't quote me on any of it... in fact, I'm anonymous... no, not ~that~ anonymous, just the one that no one knows... You never saw me...
The way to check the file is to "Search" in a text editor on "DeleteOnLastWaypoint=False" for each RGG, and make sure it's got a corresponding "DockedShip=True". Unfortunately, the lines are usually separated from each other by about a dozen other lines. You would also want to make sure that "Speed=0.000000". Some of them are "Speed=5.000000", which is the default value.