Al,
I take you at your word that your ART9 sounded great out of the box. Maybe there's something about the cart that doesn't make break in such a factor. I also agree 100% phase is worth checking, as that can also be the problem.
Going back to break in, I find the norm is that new carts break in a lot. Way more than any other component. Here's a clip from an interview with Brooks Berdan (2003).
"Brooks, do you have any caveats for readers who want to set up their own turntable?"
Yes, there are some points that I would like to stress before we begin. First, it is essential that a turntable be absolutely level during set up and operation. If the turntable is even slightly tilted, in any direction, all adjustments will be compromised and performance will be negatively impacted. Second, cartridges require 12-15 hours of mechanical break-in to allow the suspension to settle. (Sound will continue to change over a longer period.) A good dealer will break-in a phono cartridge before final adjustments are performed. Readers who set up their own turntables should readjust stylus pressure and VTA / SRA and recheck tonearm geometry after 12-15 hours of play. Third, some critical adjustments are best done by ear and when I talk about adjusting for focus, et cetera, I’m assuming the reader has a properly functioning audio system that allows differences to be heard. Don’t try to adjust the turntable to compensate for other flaws in system performance. Fix the flaws instead.
I didn't include this quote to suggest I'm right and you're wrong. Its just to show some solid evidence for break in. Brooks was very well respected with regards to TT setup, and his above quote mirrors my own personal experiance.