That just means that you have screen 2 physically plugged in to the primary port on the graphics adaptor. In Windows you have it set for screen 1 to be the primary screen, so Windows swaps them around in software.
You can either swap over the connectors on the back of your PC, or rearrange them from within Windows, either is a valid solution.
It's just down to how the properties are set up in the display options. If you right click the desk, go to Properties, and then go to the Settings tab, you will be able to alter how the desktop is displayed, and what monitor is treated as the primary monitor.
Sorted it, windows was seeing it as right but it wasnt. I had to swap ports but leave the second one out and reboot. Then i reinstalled the drivers for the main monitor and windows saw it as the main monitor then, in the new port. I could then connect the second monitor and all was well.
The problem was because ive always had the main monitor in the wrong port (before i bought the second one if you know what i mean)