VAG often disable stop/start for a plethora of reasons, anything from a tired battery to a pressure sensor. Basically the brain says 'i'm not working 100% correctly, so disable stop/start.'
What ever the actual code is will give you a better indication of the fault, bit it would be very unlikely for a faulty BCM to be the route cause of a issue. Find out what codes he got, report them back (or google them!) and you will be a bit closer to finding the issue.