My question: Why does website say the statute of limitations for Assault and battery is 2 years, but magistrate says 1yr Va. Code § 8.01-243(A)

It depends on how you want to proceed with the case. If you want to proceed criminally, which I assume you do since you went to the magistrate, the statute of limitations is one year pursuant to VA Code section 19.2-8 since assault and battery in violation of VA code section 18.2-57 is a misdemeanor. The code you cited is for a civil claim.