The same thing happens to me. It detects that I have FC3, downloads, updates and before starting it informs me that I don't have the Su-25, A-10A, F-15C, Mig-29, Su-27 ... modules.
When it loads, I don't have those aircrafts, it informs me that I have the license, I authorize it to update and download the FC3 module, it restarts and everything stays the same.