@Bobby *********
if you're married to a thai and have the two marriage certificates from getting married here in thailand, (Kor Ror 2 and Kor Ror 3), have your thai wife's i/d and her house book listing, AND proof of where oyu live here there shouldn't be any reason you need to get the embassy letter for a 60 day visit thai family extension on a 30 day visa exempt that went to amnesty at MTT.
I think there was something lost in translation with the immigration officer and your thai wife as far as what is required for what extension. BUT good luck with it