I've got a 16:9, 24 inch monitor so the sprites look a little stretched with the native aspect ratio.

Is there a way I can set the game to it's original 4:3? I don't mind having a black border to the left and right of screen if it comes to that.

I don't think you mean that the pixels have a 16:9 aspect radio, so I am confused because on my laptop with 16:9 (Windows 8.1, Nvidia), I have black borders on the left and right and a display which doesn't loop stretched.

I've fixed it now, and it has the black borders left and right, i had to 'enable GPU scaling' on the ati catalyst options and its looking better now on its native 4:3.

Thanks for feedback though, it's possible in your case you have the scaling set to default.