I have a few questions about this network:
-To clarify: the problem you're having is that users who should be authenticated by your server are being failed over to the guest VLAN, correct?
-Is there any kind of noticeable pattern among failed ports? Does the configuration of the ports that are failing over differ at all from the ports that are authenticating correctly?
-Do you have dot1x configured and working (without this issue) at another site? Can you post the port and aaa/dot1x configs from an authenticator at that site for the sake of comparison?
-What kind of database does your authenticator switch check against? Is it Active Directory? If so, what version?
-Is dot1x configured to use certificates for authentication? Are you running EAP-TLS on your network?
-Can you post the configurations of the switchports on the authenticator switch where this is taking place, as well as the aaa/dot1x global config?