I've been monitoring several stations and planets now. While the NPCs on Baltimore seem to have no problems with the docking procedure itself, NPCs at West Point are still somewhat stuck. However, they seem to break off docking after a while and move on.
Yet I have not caught any transport docking anywhere. At least around Manhattan and Pittsburgh they seem to have completely disappeared.
I'll keep watching.
I'm not sure if this is in any way related to what you're doing with NPCs, but it probably is. I made a thread elsewhere but after some looking into the problem it seems that it only happens to me and when I use a jump hole and there are hostile NPCs on the other end. If there are, I get hit with red lag where I still get chat messages for departing/new players and I still can see damage taken (if any), but I disconnect. If I reconnect, the same thing happens over again so I'm stuck until something kills me.
I have reinstalled Freelancer and the same thing is happening. I don't know why, never heard/seen anything like this before. I'm hoping maybe you'll know why this might be happening.
EDIT: Tried it again, this time it happened with no NPCs on scanners, but I was taking damage as if hostile NPCs were shooting me...
I have the exact same problem Zapp, except that it only happens to me with some gunboat sized ships, and 100% of the time with cruiser sized vessels and larger.
The station was totally locked out by NPCs for 30 minutes. Most of them (perhaps all) were junker CSVs.
Seems to only happen on the very small stations
Did you try flying ~10k away and then coming back? That's resolved the issue for me every time I've run into it. If there're no players in the vicinity the NPCs despawn.