No, no other screens enabled. Thanks for the replies so far though.
After a reboot it sometimes doesn't do it. All seemed to happen after giving my video card a clean about a week ago. After putting it back together I put it back in the other X16 lane, since this is directly under the mahoosive case fan. Once restarted it didn't seem to recognise any ATI drivers so after an unsuccessful tinker I reinstalled them and although better I do get one or two other problems, I'm starting to think this all links together.
One is the desktop might decide to change resolution and the other is it occasionally loads up the window asking me if I want to enable crossfire (have the xfire profile drivers). I thought it already was since it is set to standard, anyway the fps would suggest that it is.
Small, intriguing and annoying little quirks going on so my guess now that this is maybe a driver issue.