Never Mind I had inadvertently hit M which mirrored the canvas it is fixed now. Thanks anyway.
The overview window seems to be the one that is getting exported as a .jpg but it is the opposite horizontally to the Main window, what have I done wrong? I want to export the Main window not the overview and I'd like if they the overview and Main window were the same.

The overview is actually showing you the original direction, you must have mirrored the view of canvas instead of the image, just look at your layers (key m is the default to mirror horizontally the view of the canvas), if you want the image to be on the direction you have on the canvas just go to the menu bar and under image you will see the option "mirror image horizontally".