I get this as well sometimes. I think it may be due to some conflict with the monitor numbers between AMD CCC and Windows 7 "Screen Resolution" settings. I'm thinking it may be a issue with the latest AMD video drivers
With 3 monitors, it also switches the order of my main center #2 monitor and the far right #3 monitor.
By chance, have you been changing how (ex: HDMI, DVI, DisplayPort, etc...) the monitor is connected before this happened?