Some tuners find it hard to track at low frequencies, similar to tracking of digital pitch effects.
Also without a locking nut the note produced when you hit the string will "bounce" going from higher to lower then rest at the normal. As the initial note you hit will change so much the only fixes/things that help are using a locking nut, Use thicker strings (or anything that will give you higher tension).
Try not hitting the string so hard when you tune the note, this will reduce the amount it goes out of tune when the string is initially hit :)
