I had this problem too, sometimes.
I don't understand something. Between the ATIS information and the taxi request, there are somme minutes. During this time, the weather can change a little. Ok.
But after the Ground Control give the runway to take off, it's not right to see this problem, for me. Ground control can't give a different runway for AI and the player and and I suppose it can't change the runway all the minutes

Same problem when the player is in final for landing : it's abnormal to see AI Aircrafts takeoff from the same runway in opposite direction. It's very dangerous
I don't say this is due to PFE, but I had this problem too.
Luc