Hey great news, I think I found the solution! At least it works for me :yahoo:
My first impression was good and I didn't need to go through the tedious process of enabling/disabling each of the 8 previously mentioned suspects individually: the cause of my problem was FSUIPC. After enabling everything else and refusing access just to FSUIPC (with a fresh and untweaked FSX.cfg file), I earned my certificate without any problem. It even stays there after restarting FSX, which is what we wanted I guess...
So now, the only thing left to do for me is restoring my backed up FSX.cfg file and find a way to not have FSUIPC interfering with certificates (expecting the problem isn't caused by my tweaked FSX.cfg file, but after these tests chances are slim). I'll report what I've found to FSUIPC support and some forums where people were left helplessly with no solution.
Thanks again for your help !