I recently upgraded my Subversion server to VisualSVN Server 2.1 and started experiencing this issue again:
svnsync: OPTIONS of 'https://xxx/svn/TentacleSoftware': Server certificate verification failed: certificate issued for a different hostname, issuer is not trusted (https://xxxx)
It looks like the account under which the VisualSVN Server service runs has been changed, breaking my account profile work-around.
Some digging in Google revealed a more elegant solution to the problem; specifically set the configuration cache directory in the command line to a static location, so that any saved/accepted certificates are persisted between accounts.
As my normal user account on the server, I ran the following command: