There are a few things to keep in mind here, when moving from a prepro to a dedicated preamplifier.
The pre/pro uses its digital EQ to change the properties of the sound if you run the auto-calibration. This allows it to attenuate or augment high/mids/lows as they negatively effect your room to create a more "balanced sound."
Of course, this digital EQ, and using a pre/pro usually doesn't bring the music into the room as well as a dedicated 2-channel preamplifier; especially a vacuum tube preamplifier.
You mentioned you changed the tube? Did you change it to the SAME tube, or did you purchase another tube from another manufacturer? Are these newly manufactured tubes, or are they N(ew) O(ld) S(tock) tubes?
Tube rolling can completely change the sound, ESPECIALLY in the bass region. For instance, my RCA 12SN7 tubes present the bass in much the same way as you are describing which is in abundance, but sort of muddy without much articulation. However, my Sylvania 6SN7W short bases, give me bass that is super tight and punchy, but at the cost of a loss in output.
If you did try a completely and tube, and experienced the same exact thing, perhaps there is a problem.
Its also possible that the LS-9s are just too big for your room, and without your pre/pro attenuating frequency response, you are still overloading your room. The sister crossover on the back doesn't attenuate higher mid bass regions; it just curtails the response at the very very bottom of the range. So, even though you have it set to small, its probably putting out mid-bass in ridiculous amounts and this is causing muddy sounds and mid-range smearing.
I've been dealing with this problem since I got my LSs as well.
