Kleopatra seems to use the "keyserver" entry from gpg.conf to enable
the automatic key lookup via fingerprint from a smartcard. Thus if
the keyserver is only defined in dirmngr.conf this auto key fetch does
not work. It is a bit surprising given that the standard keyserver
lookup works anyway.
Suggestion: Check the keyserver option from gpg.conf and from
dirmngr.conf and enable the auto key fetch if either of them exists.