I'm surprised you're seeing the error about duplicates- normally the first error (about the missing SharedSSMS file) would stop SQL Source Control loading.
I'd suggest running a "repair" of the SQL Source Control installation from the add/remove programs option in Windows to see if that fixes the first error. For the second error, try unlinking your database, restarting SSMS and then relinking. That may well fix it, but if not, please email our support team (firstname.lastname@example.org
) with details of the error (send in the error report with your email address when prompted as well) and they'll be able to help out.