I'm not sure the problem is AF2k9 or Windows. I think it might be the user this time...
You know, WinUAE is a fantastic piece of software and Toni Wilen should be commended for his efforts considering it is free. I wish some of these people -especially the 'if you don't own real Amiga hardware you are a traitor to the memory Jay Miner' group- would take a long hard look in the mirror. Toni has done more to keep the memory of the Amiga alive and relevant in today's world than most of them combined.
I think Windows XP SP3 would help your AF2k9 problem. I believe that SP3 is ~300 meg so you could always download it somewhere else and transfer it on a USB Memory Stick.
-P
