@Alumni said:

I don't know. I don't play guitar, and I'm definitely no gearhead. It could also have something to do with the new sound guy, whose background was a bit different than Phish.

Garry runs FOH (front of house) sound and is responsible for the mix that comes through the P.A. Trey and his guitar tech are responsible for the sound that comes out of Trey's amplifier(s) - aka "tone." In theory at least, none of what Garry does should impact Trey's tone at all - volume certainly, but not tone.
Just as a clarification...I thought grey had been using the compressor again, since 2010 or so...and his sound is infinitely better than 09. Loved 99 tone, btw
Far as I know, there have been no major changes to Trey's rig in quite a while, and I hear the same tone that I've been hearing since the Ocelot hit the scene in summer 2010. Sometimes I think it gets a little too up in the mix, and cuts through everything to the point where it may irritate some audience members. This then gets explained away as a tone problem.

I really liked the 1999 compressed sound a lot too, fwiw.