Paul Reed Smith, Guitars. Years ago when I had the chance to play one of the first few that were ever made on a stage... It sounded like a million bucks! I am not sure if they would sound as good as they used to but from what I know, they are very top quality guitars. I wouldn't think that a PRS would be the reason for a bad sound. We all know that Alex can play like a mother fucker so I would rule out the guitar for the "bad" sound.
Hughes and Kettner amps are what he plays thru also... I have had a H & K amp for years... a buddy of mine has one that is identical to what Alex plays thru... They are great amps and they sound awesome... Pure Tube Amp. Powerful as fuck! But they can be tricky for a sound man to make sound good in the front of house... That was the problem that we (my band) had with my amp... What it finally took was me adjusting the board while I was playing during a sound check.
What basically happens is with an amp like a H & K, most sound guys are used to mixing a Marshall or a Fender... a typical amp, in other words... The sound man needs to get in tune with what the guitarist is hearing in his head... The H & K amps are not as "forgiving" as a Marshall or Fender or a chainsaw amp (something solid state). Also, Hughes and Kettner has what they call a Red-Box, which is built into their amps... This allows you to run directly out of the amp instead of miking it. They sound really good but in turn being as clean with running direct can be hard to make sound good also because you have to run the amp at lower levels because it is such a clean, direct sound. Most, no, ALL amps sound better cranked up and running hot... You can do that and adjust with the miking situation, you can running direct.
I am thinking that the real problem with his "muddy" sound is the fact that they didn't have time to prep correctly and also they are playing outside... which can be really tricky to get sounding good when recording. The soundman has a board mix for the recording but if he is trying to mix for the audience, live thing, then the mix for the recording side can get a little screwed... if that makes sense.
Whew!