Thai visas have always been a PITA.
Most doctor offices do not have a notary on staff. A medical doctor is not going to travel with you to a notary. Notaries will not approve unless the doctor is there. Ah, welcome to the TAT.
There are a few options:
1) Keep trying different notaries and hope one is willing to bend the rules.
2) Ask for a jurat (affidavit), but it may not be accepted by the Consulate.
3) Contact the Consulate and ask for advice. I wouldn't hold your breath on this one.
4) Wait until you are in-country and pay an agency to help you with the documents, etc.