Ok, I double check that the whole addon manager folder is excluded from the antivirus and added it as excluded just in case again, then run the live update, with no change. Then I also did a full reinstall of GSX, with no change either.
I wasn't feeling like reinstalling windows as well, so I wanted to try some other things as well. And I have noticed that half of my products were listed as installed and active, while half were listed as installed, in trial mode, despite having the serial added in the addon manager. And I was still getting the message that a few of the products were installed and need to be activated when starting P3D and the licence wizard for CLT and FLL after I quit. Then I tried and went from full screen mode to activate the licence via the licence wizard for CLT and FLL (again, despite being listed as active) and then went back to the sim, when additional messages started to appear about the other products previously listed as in trial mode. Now all of them work again, hope it stays this way and that I will stop getting licencing messages every time I start P3D
Thank you for the ideas and help, hope this helps someone if they get in a similar situation.