Same problem here.
I uninstalled all FSDT products and deleted all virtuali and addon manager data files that I could find. BTW, registration information was retained? I'm not sure where that is located.
I reinstalled them all.
I landed at KLAX, and then only added SafeDock TS24 wall mount to all gates, and went to gate 207. All visible gate indicators were showing correct ids. Saved flight.
Reloaded flight and all visible gate indicators now showed 9.
This seeing correct gate IDs and then having them change on reloading has been there for me since version 2 came out. Flying into a previously visited and modified airport always has gates with a single ID. Yet the customize airport window shows the correct ID as well as the jetway customization window.
I wonder if it some interaction with changing the docking system? I have routinely changed the docking system when I arrive at a new airport.