The problem might not be on the PC/Windows side...
On the Amiga side, what CD filesystem are you using in Workbench/AmigaOS?
Also, which ROM version are you using in WinUAE, and with which version of Workbench?
Try a 3.1 ROM with either Workbench 3.1, 3.5, or 3.9, and try using the CacheCDFS CD filesystem which comes on the OS3.5 and OS3.9 installation CD's. As alternatives, there are also AmiCDFS and AsimCDFS on Aminet.
Steve.