VAT not being removed when adding a number to businessTaxID
Commerce, by default, uses this library for VAT validation.

That library is just a wrapper for a European SOAP endpoint for these types of things at http://ec.europa.eu/taxation_customs/vies/checkVatService.wsdl

The error code MS_UNAVAILABLE that endpoint can return says:


  The Member State service is unavailable, try again later or with another Member State;


So I'm guessing an invalid member state was selected, or they are having some technical difficulties on their end.