On my camera (D300) there are two settings: one to set the auto-rotate 'flag' and one to do the rotating. You can set both, either, or neither. e.g. I have auto-rotate set, but prefer to preview the image unrotated on my LCD, for maximum size/resolution.
As far as I know, there is no setting in Bridge/ACR to over-ride auto-rotate. Maybe there is another setting on the D80?