Nerve60 exactly what type of “rounds” did you play to figure out the BS settings?
If all you changed to correct the issue was to alter from using a Full BS to a 1/3 BS then the issue is probably not that headwinds affect ball flight differently on PCEA vs. Flash.
The issue is more likely that the Apparel Enhancements (specifically the Level 7 Swing Edge Shirt you wear) in the new PCEA version is increasing the amount of Backspin you generate with your irons.
Now I get that you corrected this by adjusting the amount of BS you put on the ball, but you also need to remember that if you happen to play in a WGT or CC Tournament where the Apparel Enhancements are disabled and you use your new BS settings you may start to overshoot the hole as you no longer generate the same amount of BS. The Apparel Enhancements do not work in all types of games. They are turned on in Head 2 Head, ranked or practice rounds, showdowns, clashes and turfwars. In WGT and CC tourneys they are turned off.
You might want to try changing your shirt to the basic shirt that has no enhancements and see how Full BS and 1/3 BS affect the balls distance in both a Ranked round and a WGT or CC Tournament .