Something I run into when trying to tune an acoustic through any tuner (I usually use a very expensive Peterson StroboTuner and not one of the cheaper ones) is ambient noise getting into the mic and causing the strobe to bounce all over the place. I found that a good hypercardioid mic up closer than I'd normally mic an acoustic to help. Usually one of my Neumann TLM103's or an AKG C414 with the right pattern selected.
Just be thankful you don't have to make fine adjustments for intonation on an acoustic like on an electric using a mic
