Have you checked the calibration of the tuner ?

I once inadvertently changed the calibration (away from A440) after a particularly busy recording session. I came to lay down an over dub and was totally mystified by tuning ! The first two guitar tracks were tuned to A440 and the third one to A447.

Took me a while to figure out want the problem was !

Check out the part of the Manuel that deals with calibration though I would imagine a swift factory reset will also do the job. If you do go the factory rest rout you will loose all your user patches unless you back em up. I don't know if this is a problem however I figured it was worth mentioning !