Is this something to do with having two .exe files in your P3D folder? If you use FS Estonia migration tool, you will have FSX.exe and Prepar3d.exe in your root folder. Try running P3D.exe and check to see if your FSUIPC is registered and you get all the lovely functionality, then close that and check out the fsx.exe by running that, and check the FSUIPC registration status.
I had this very problem, in that I ran the fsx.exe first, and saw no registration, despite the FSUIPC and WideFS 'check registration' routines running perfectly well on installation, and then found that by running both exe files one after the other, the FSUIPC registration became recognised by both versions.
I hope this may help,