Thanks for all the replies so far, in answer to the previous one:
-I don't think there are any programs causing the problem since I hadn't installed, or really changed, anything (at least not that I recall) when the issue started.
-If I change to any theme it adopts the wallpaper but says I'm in windows classic (but some aero effects still apply)
-I have some clean-up software but it's never been an issue.
-This problem occurred around the time I installed the other graphics card. Although not straight away. Before that it worked fine.
One weird thing is there is a transparent, aero line running along the top of the taskbar. The start menu isn't aero. Also, if two labels combine in the taskbar (i.e. having two of the same window open at once) when I click on them the text is invisible. It's all very frustrating, I can't even change to windows basic
I appreciate the help!