Why are the reference alleles different from what I see in the literature, for example, A for T for MTHFR C677T?

Alleles are listed in the orientation reported by StrateGene. Sometimes that orientation is the opposite to what is commonly employed in the literature: thus a different allele. 

As a rule of thumb, A may be replaced with T or vice versa, and C may be replaced with G or vice versa.