A string only has a certain amount of energy, and how loud you are depends on how fast the energy gets dumped into the air. Banjo dumps very fast (dumpster banjo effect?).

Most tuners "select" what the note is, from all the crud and corruption, by ignoring anything that doesn't last longer than a certain "filter interval." The banjo "plunk" may just not hold a steady pitch long enough for the tuner to realize it's a "note." Almost any instrument has more "sustain" than a banjo, and tuners work better on sustained, steady tones.

John