I have these pops & crackles as well... but irregularly. The strange thing is, it can occur and be very evident. And then, other times, it works with no crackles or pops. Could this be a soundcard issue?
My soundcard is set as slave (external).
Have you resolved your crackles problem ? i've got those too !
My sound card is also set "external", no way to have sound from spdif with internal.