It confounds me as to how only the phono-stage can be affected whilst the AUX can sound as beautiful as ever at these times?I don't see that as surprising. Unpredictable, yes. But surprising, no.
As you certainly realize, the phono stage uses circuitry that is not involved in the processing of Aux or other line-level signals. And that circuitry is vastly more sensitive, in terms of the signal levels it is designed to process, and provides far higher gain, than the line-level circuitry in the preamp.
Best regards,
-- Al