You nailed it. The bass was so muddy that it masked Kevin Eubanks' playing. Without prompting, I asked my wife "what do you think of the sound?" She answered "It sounds really muddy". I asked the man next to me (who was a donor) whether he thought it sounded muddy, and he agreed. We both decided to move.
I went down to some open seats in row G and it sounded better, but still a tad midbass heavy. I don't think it was the room, I think it was the soundboard.
I don't agree that different venues can't have good enough acoustics that groups can sound similar. I've heard Dave Holland in at least 4 venues of varying sizes and shapes (Koncepts, Yoshi's Oak and SF, Palace of Fine Arts). In all previous cases, one could hear Dave's bass sound as very similar to what you hear on CD, only more live (duh) and dynamic.
What I experienced at the new center reminds me of another place I visited when it just opened. If anyone remembers the short-lived jazz venue "Storyville" on Fulton, I saw Wallace Roney and Geri Allen there if not on opening night, then right afterwards. Low ceilings, lots of tables, lots of pillars, tiny place, lots of energy being so close to the musicians. The sound was terrible until Wallace got on the soundboard and tweaked it so that his wife sounded better, and the cymbals weren't so hot. He didn't look too happy about needing to do that, but the sound guy was doubling as wait staff.
I want everyone to know that I did speak to management, and hopefully they have fixed this. I don't mean to turn people away from this venue, in fact, I want it around FOREVER. I am going back for the Afro-Cuban All Stars on Sunday, so I'll let y'all know.