I spent some time with this on the oscilloscope and realized that the problem is my status line from a LIPO charging circuit. It's connected to I34 which is the VDET_1 line input and one of the inputs to SAR ADC1. That is where the square wave is coming from - in this case oscillating between High a...

I'm digitizing a short audio signal using IO36 (A1_0) at 20Khz with the code below. It works on an Adafruit Huzzah32, but not on my prototype board. I'm trying to figure out why. I'm seeing a 347 Hz square wave coupled to the actual audio signal. The square wave does not show up on the pin on an osc...