You know, I had a similar problem with my phono stage for a short time, and I was going to send the Pre back to Cary when I too realized I had rolled the wrong tube into the wrong slot on the phono section. I had the 12ax7's on one side in the 12au7 slot, changed them back and it sounded perfect again.
I'm not familiar with your preamp from looking at your system, but could that be it? Is it a tube pre? If so, try uninstalling and re-installing all of the tubes.
I'm not familiar with your preamp from looking at your system, but could that be it? Is it a tube pre? If so, try uninstalling and re-installing all of the tubes.