I'm sorry, but there's nothing in the Addon Mangager code that interacts in any way with the logbook. I tried it, enabling just the Addon Manager, and the problem doesn't happen.
However, I tried with both GSX and the Addon Manager enabled, and yes, I can reproduce it, and it seems to happen ONLY when starting from VHHH.
This might be related to the fact that, in order to allow to pre-select an airport while in flight, we must ask the sim the list of the airports in the area. We only ask the sim of course, we don't try to touch any files and surely not the logbook file.
So, it seems that you simply discovered a P3D bug that, if an application ask for a list of the closest airports, it might confuse the logbook, no idea why it seems to happens only there, but we might ask LM to look into it.