The putty installed on windows does not appear to be the latest and does not support PKCS11 and CAPI ssh keys on hardware tokens.
I was however able to manually change the putty client installed in source tree tools and get hardware pkcs11 keys to work perfectly.
The sourcetree ui only supports the putty tools for loading software key files. However if you can run the newer pageant and load keys from either CAPI or PKCS11 among other ways to authenticate:
