That's weird. :o
I've never, ever had a problem with my HD500 (which I've had now for 6 months), nor with my PODXTLive.
Both Tuners work great as "tested" by my ear and my bandmates.
Not saying you specifically are not having a problem though. :P
My best guess is (as stated above) the string is old and flat thus not giving out good vibrations. Also being that the third is un-wound can be problematic for it's pitch.
Seems to me the calibration and reference is set with a crystal circuit. The Tuner can be set differently per page 1-4 in the Manual. "Reference (Knob 1): If youâ€™d like to tune to a reference other than standard 440Hz, select from 425 to 455Hz.".