If so, though, I should be able to compensate for
that. What kinds of things
could I do to the signal to make it more acceptable?
Have you compared the outputs with an oscilloscope? It would seem to me
that five minutes with a scope would solve any problems you might be
having, as any distortion in the signal caused by digitizing it would be
obvious.
My two immediate thoughts are: if it's "pulses", maybe the quantization
is causing issues; or maybe the sample rate (or some other randomness)
is introducing noise to the signal.
Also, a scope should tell you if there's clipping or other analog
problems (from overamplification, say).