Wow, that's really weird. I pulled out my old system Saturday with your same setup and also couldn't get the drive to work in Winuae. I forget what version I originally had, but, I upgraded and still couldn't get it to work. Even though I can use the utility to create .adfs from the floppy and CW_Config.exe shows the card and the drive, kb, ports, etc.
I can mount it but it just keeps saying there's no disk in the drive even though there is, and I don't get the clicking sound anymore.