By default, in manual mode the rear dial near the viewfinder changes ISO, the rear dial under the top LCD (I think Phase calls it the side dial) changes aperture, and the front dial changes shutter speed (the dial nearest the readout on the top LCD for SS, ISO, or aperture changes that parameter). These can all be reassigned in the camera setup menu either from the Phase digital back or on the top LCD. If your camera does not work this way the dials have been reassigned on your camera. You can either reassign them to however you want the camera to work or reset the camera to defaults. There was no change to this behavior with the recent FW update.
In order to make it function like a default Nikon, assign the front dial to be aperture and the rear (side) dial to be shutter speed. This is how I have mine set-up to keep it consistent with my Nikon and Sony cameras.
