Are you sure that the earlier recording you used for comparison was from the phono (RCA) outs? Maybe you had used the headphone or main outs before, and the RCA's were always a bit naff? This one is really a headscratcher. I can't think of why the RCA out would be the only one with the problem. I wouldn't have thought any additional circuitry should be involved. It's just another line out.

And why specifically the negative part of the waveform is distorted, but NOT the positive..? Strange. I'd still like to see another 3k do the same test.

You never know...