THE OFFICIAL BLOG OF THE SBS DIVA

For background see - http://social.technet.microsoft.com/Forums/en-US/winserveressentials/thread/6946b2f1-283d-4a09-b939-40acb3cafdfa/ and http://social.technet.microsoft.com/Forums/en-US/winserveressentials/thread/bd3b025f-076b-4fb3-8cf2-883f1643c2aa/#8c35f734-1c72-42e2-8815-e6bb15cbbf03 

So you deploy Windows 2012 Server Essentials.  And stuff happens.  And when the machine starts to act wonky you go "I'll do a sfc /scannow to see if there's any files to repair".  And that act replaces files on the server - specifically in the web config files - back to their uncustomized defaults.  And when you do that RWA no longer works.
 

Resolution:
The "C:\Program Files\Windows Server\Bin\WebApps\CertWebService\Web.config" configuration file had an environment variable %SBSPRODUCTBINPLACEHOLDER% instead of the absolute file path such as "C:\Program Files\Windows Server\Bin".
We replaced all the instances of %SBSPRODUCTBINPLACEHOLDER% with C:\Program Files\Windows Server\Bin.

With the above steps, we were able to correct both Connect Computer wizard and RWA not browsing issue.

The moral of this story is don't run sfc /scannow as we know that for sure triggers the issue.  The most recent case the person did not run sfc /scannow and thinks that something that was installed may have triggered this resetting.  Unfortunately we're not sure exactly what.

At least we have a way to fix it, but it would be nicer to prevent this from happening from the get go.  But for now, be aware of this behavior and it's been bugged with the product group.