Tuner/Tuning Question

Another newbie question! :)

So I sat down tonight and tuned my vintage 3-string DAA for the first time using both my Snark tuner and the Harpkit online tuner on my phone.

Weird thing is, I can tune my melody strings to A3 and have both the tuning program and the tuner agree, but when I set the bass string to D3 according to the harpkit tuner, it ends up being read as F# consistently by the Snark tuner. If I set it to the Snark tuner's idea of D, it sounds off. Not sure why it would only be that way with one of the three strings? I clip the tuner on the head, making sure it doesn't touch any strings, of course.

I've gotta say, too, that I can play Go Tell Aunt Rhodie on the melody string alone in Ionian and have it sound fine, but the moment I add those other two strings as drone, the result sounds awful. Nor do the strings appear to be slipping out of tune. Hmmmm .... any thoughts?