Ff... how have you loaded the Ref 3 outputs, other than the Ref 110? If you have hooked something else up to the Ref 3 outputs (e.g., a subwoofer), other than the Ref 110, what is the input impedance of the other devices? What phono and CD inputs are you using?
Also, if it's not too hard, I would double check the bias of the KT-120 tubes and make sure they are all lit up. Power tubes drift the most when new.
Just trying to cover the obvious. If you call Cal at ARC, at least you can tell him that you covered the regular bases.