I launched both from the stock launcher and the bms.exe and did exactly as you said and the registry still would not update. also checked my theater.lst and it is still populated appropriately. I did a fresh install of BMS and just overwrote the Falcon BMS 4.33 U1\Data\ folder with my old one with all the theaters and campaigns and everything works as it should. so the issue is most likely something injected into the config files, maybe.
I wont be reinstalling your launcher for a while as I have some BMS events coming up this weekend. but a minor bug report: The launcher CTD when you double right click anywhere in the “KeyMapping” tab. possibly other tabs as well.