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I think what you might be seeing is the ripple in the output due to the D to A converter. The circuit uses a simple pulse width output and some filtering to produce an output voltage. The output has a .1v ripple at 16.6kHz. See the two photos of my scope traces:
http://thingiverse-production-new.s3.amazonaws.com/renders/20/ae/58/14/bb/output_ripple_1_preview_featured.JPG
http://thingiverse-production-new.s3.amazonaws.com/renders/85/fb/ef/f4/93/output_ripple_2_preview_featured.JPG

I would use some additional low pass filtering to reduce this ripple before sampling at the rates you are using.