Well it's been a while, nobody answered my question, and I forgot about it.
Then today I faced the same problem on a different project, googled the issue and the only person who seems to share my pain is...... me, from 8 months ago.
However this time I've solved it!!
The fix is, in Visual Studio (using 2013 here), with your solution open, go to File / Subversion / Change Source Control
and browse to the correct SCC Binding Path
for your solution folder. Click Connect
and it fixed the issue.