To Further elaborate.
I have already removed all other tokend from the /Library/Security/tokend folder. Only the PIV.tokend remains.
I noticed, in Keychain, if the PIV keychain is unlocked I cannot use any application that requires access to the certificates to authenticate.
My workaround at this time is to quit the application that needs access to the certificate, remove the card, re-insert the card, and launch the application. The application will then prompt for the PIN and work properly.