Site has quickly resumed it’s old ways and because I’ve just added this site it is clear where the issues are. GoDaddy is having difficulty with a WordPress site and a MyBB forum at the same time. So much for the professional package. Looks like I need a different package per site. Alternatively I need my own server. I’ll look at that.
In the meantime I’m going to move the sites around. I’ll move the forum from GoDaddy next week and just leave this site and after a couple of weeks I’ll bring back the files section. See if GoDaddy has the oomph to manage that.
Update : 1-Apr-2015.
Looking at issue and it seems there was a problem with a plug ins connection to the DB server. It was holding on to the links until they timed out and thus everyone was locked out until the DB server timed out.
Managed to fix it by luck and with no help from the GoDaddy support team. The WordPress team had raised this as an issue on their blog and when I went to upgrade they suggested a couple of tests and the culprit was identified.