The SBS 2011 BPA was showing a bunch of network errors including the IPv6 disabled warning. This is an extremely annoying error because there is not enough information to track where it comes from so it caused a bit of head scratching before I found the root cause.
I am using Fortinet Client Lite and it had installed a miniport network adapter which I was unable to configure nor delete even after un-installing the Fortinet Client. The adapter is visible with device manager. A search of the registry for “Fortinet” uncovered the Fortinet Miniport Adapter which I deleted. I re-ran BPA and the annoying IPv6 message was gone.
If you are not using Fortinet Client and still face this problem. Check the Network Adapters in Device Manager and make sure that they are all configured correctly. BPA seems to check all adapters even the disabled ones.