Please run HDToolbox and check if the drive is listed there. If it is, click on Install Drive -> Create New -> Read Configuration and write down the determined values. Then go to WinUAE and do the same. I'd guess in WinUAE the drive is defined smaller than on the real Amiga. You might be able to repair this if you run DiskPart and use the Clean command on the CF card before you add it to WinUAE. If this does not help, you'll probably have to install it on the real Amiga and not in WinUAE.
If it is not listed in HDToolbox, then indeed something might be broken or incompatible. It's more likely that the CF card is incompatible than that the adapter is broken, though.
