Is there any correlation for time of day? Maybe there is a difference in the power quality feed into your premise based on something else happening around your local grid? A long shot I know.
Since you have controlled for so many elements, the most likely culprit to suspect is YOU. I would set up a controlled blind test with an audiophile friend so you would listen to the system for 10-minutes on at least 4 separate occasions without knowing if the system was just turned on or if it had been on playing music for an hour or more. If this proves the effect is not imagined then I would sell all my equipment and move.