On Mastodon's old forum they had a big thread about it. But yeah, basically CtS wasn't played super well, I remember The Last Baron in particular being a massive clusterfuck. Then the band went offstage for what felt like a lot more than 10-15 minutes. The rest is as slap said.
The thing is, that fest had been like 7 amazing bands all playing incredible sets before Mastodon. Baroness tore through their flawless set without saying a word, and High on Fire obliterated their hometown- the show was in Oakland, and I think it still might be one of the best times I've ever seen them. All Mastodon had to do was do their thing and it would have been gravy, but Brent threw a bitchfit and derailed it. That, combined with the fact that Mastodon were just not a very strong live band at the time, just left a really bad taste in everyone's mouth after the show.