Hi Chris,
Thanks for the prompt reply. We're working on taking the FFT now and we'll see if there are any harmonics. When shutting off the ADC (via the crystal), we do see a noise reduction on the noisy channels. Also, when disabling CLKOUT, we also see a noise reduction.
Interesting note, we changed the ADC registers to use the external outputs (no longer using internal multiplexer CONFIG0.BYPAS = 1) , we do not see any noisy channels. This might suggest that we don't have interfering clock lines.
Let me know what you think. Thanks!
-Martin