Hi,
That is surprising, yubikeys should be fully supported.
Are you sure that you are using the correct public key?
Yubico has sent me some test yubikeys which are currently in the mail. Once I get them I can test it and might know more. But other Gpg4win developers have tested it already and found no issues. Except that it might be problematic to switch between Yubikey apps. So if you are using yubikey also for something else there might be a conflict.
We have improved that in our current development version but that will be released earliest next spring.
Best Regards,
Andre