My patient has all the signs and symptoms of a MTHFR defect but no SNP, what gives?

Even a "normal" gene can express altered enzyme activity. Look at the regulatory factors for that gene: Perhaps your patient has heavy metal toxicity, lack of cofactors, chronic infection, etc that are affecting the gene, even in lieu of a SNP. Another factor to consider in the clinical evaluation of gene performance is to look at the weight of epigenetic control factors.