I suspect that the new audio engine in v3 (the whole point of v3) is responsible for the improvement.

The Bur-Brown DACs and the DSP chip all claim to handle 48KHz inputs/outputs, and the input to it all comes from the processor chip (software).

EDIT: Ah.. found it. empeg_audio3.c appears to do the actual audio-data output, and it seems to be fixed rate at 44.1 from the processor here. So any artifacts you were hearing must be from the empeg player software conversion to 44.1 before handing off to hardware. v3 appears to do it better.

Cheers