Well that was odd, I spent a while trying to figure out how to disable the second gpu on my card from the CCC, (I found out I could do it from the device manager, but I didn't wanna do anything I might stuff up and become permanent), I had to disable catalyst AI to stop the crossfire, but I still couldn't find the setting which is either me being stupid or it's just not easily found (i do remember the setting on older versions of CCC but not on the recent ones), meanwhile I had made a setting for SS2 in the CCC, so that when I figured out how I could change to using 1 GPU, it was ready.

I updated my drivers to the most recent one to be sure (which was just one version different), then accidentally ran the custom program which got me into the game, and...the graphic issue I was having has gone, which is strange because it was the same as the default setting I was running before.

Thanks for the advice.