Only on a couple occasions recently, I've noticed a discrepancy in the runway numbers given by the SID & STARS section and the runway marked on the tarmac and recorded by the flight sim addon modelers. It's only by one number, say 26 instead of 27 or something like that. Is this a problem with PF3 or the model of the airport do you know?
If it's PF3, let me know and when I come across it in future, I can report it to you for correction in a future up-date.
Is this not mainly a problem between magdec and scenery? Whatever is written on the tarmac frequently differs from the ATC declared direction. PF3 picks up all its info from runways.csv. So if it's wrong there PF3 will of course repeat the error.
What I would suggest is to look carefully at the offending runways you have mentioned to see if there is indeed a discrepancy between the magdec direction and the actual rwy markings. If you have DXTbmp you can easily change the runway markings if they are wrong. Otherwise it would be a change in magdec.