This issue appeared for me with version 1.15.
Now, it’s almost every time. Upon startup (of MSFS that is) any aircraft that was not part of my Standard package, is absent from the plane selection screen.
Meanwhile, going to my profile and Content Manager, all of the additional planes are properly listed.
If I quit MSFS and restart it immediately, all the planes are properly listed and available.
Please note that the additional planes I have were all bought from the in-game store. I also have nothing in the Community folder. The additional planes are the MB-339, the T-45C and the Top Rudder 103.
When the problem occurs, the game is functioning properly. The planes are just missing from the selector.