This is almost certainly a problem with FSUIPC, rather than PF3 - you will see from this link that I had exactly the same problem (and I'm not the only PF3 user affected):
https://forum.simflight.com/topic/98465 ... -start-up/
John Dowson has provided detailed information in the FSUIPC Support Forum on addressing various issues caused by start-up timing with 7.4.12.
Please look there for a resolution to your problem - you most likely need to delay the initial connection to restore reliable hotkey operation.
I hope that this helps,
Martin