That certainly sounds like it could be an RDB issue

What I would do to test it is this.
1) open WinUAE as admin.
2) Try the CF as admin, just to make sure that windows isn't causing any issues reading the card too.
3) If this fails then load what ever version of WB (set it to something like DH3) you use and also have the CF as a second hdd HDD.
4) Start UAE and hold down both mouse buttons on boot and select boot options.
5) select DH3: and let it boot and see if it allows you to access the data on the drive.