No sorry I must not have made myself clear in the last post. Changing the mouse didn't fix the problem. I tried another mouse and the problem was still there, changed back to the original mouse and half an hour later the problem stopped. Having turned on my computer today though and the problem is back. Even without the mouse plugged in the window I have selected flashes as if its been deslected and reslected i.e. as if it is quickly changing to another program and back.
My mouse is a logitech not sure of the exact model but it definitely didn't come with any software. Computer is custom built - Intel Core2 Quad CPU @ 3ghz, 8gd ram.