Well...as bassists we are all familiar of how difficult our frequencies are to manage. It seems the bass is almost always either hopelessly buried or dominating the texture in most live situations. So the sound man might have just been having trouble with the acoustics of that venue.
However...
In Tool's case I can see how their signature sound/orchestration could contribute to Mr. Chancellor's bass being obscured. For one thing, everyone loves their drummer, so that double kick is gonna be pumpin' through those subs (pretty much obliterating everything in it's wake). Also, Justin Chancellor plays in the upper mid range of the instrument a lot, with a pick, and plays chords pretty frequently, so it's sometimes hard to aurally separate the guitar from the bass. But, there's no doubt about it...Justin Chancellor is one bad mofo!
eViL cAkE
But Maybe it might have been where you were sitting for the eq, or maybe you werent to used to his sound because from what I know, it cuts through allmost anything(I've used it alot with my band, cranked mids and highs and the low's at around noon.). His chords sometimes blend with the guitar but even then the chords still ring through. I used to be a huge Geezer Buttler Fan(Still am) but Justin gave me a new perspective on playing bass.
