I find that very strange. As LIRZ has only two runways 01 and 19. It's far more likely to be problem with your afcad file(s) rather than PF3, and whether or not you have updated PF3.
JohnY wrote: Yes, well, there is definitely something wrong with LIRZ Sanegidio Perugia.
I've just tried to fly from there to LSGG Genoa and it gave me a variety of runways to take off from that don't exist!
John
You need to provide the logs for that flight.