how was it addded as a drive in WinUAE? as a PC driectory mounted as a drive? on the uaehf.device (or whatever it is)? or on the IDE0 device to emulate the A600/1200's IDE?
i've seen this before. i ended up having the drive plugged into the IDE on an A1200, and booting off the 3.1install disk and running HDtoolbox from there. it found it, and partitioned it from there.
maybe setting it up on the PC from within WinUAE with it set as a hard disk on IDE0? maybe plugging the CF card into your adapter and into the IDE port on your PC to force the card into disk mode?
weird, as i've not had trouble with other sandisk cards, or the cheepy noname CF cards i got from Maplin...