jremington:
When the microphone is pointed at the source, you are probably overloading the microphone amplifier, which leads to serious waveform distortion and totally incorrect frequency indications.Post a clear circuit diagram (not a Fritzing mess) of your microphone input circuit.
I'm using MAX4466 with Adjustable Gain.
You can see the circuit diagram here: https://cdn-shop.adafruit.com/datasheets/MAX4465-MAX4469.pdf