I think partially it's due to whatever processing they're doing on the microphone signal. LALP is not all that much different, there's parts where the vocal audio is very distorted. My personal theory is that they're trying hard to both accommodate his belting and a few seconds later his super-breathy voice. The only way to have both at audible levels is to compress the living shit out of the signal, and I think that's what we're hearing.
In LALP, for sure. Though I'm not sure it's the same issue as in Chaos in Motion. Didn't someone clarify that it sounds bad because of overuse of Autotune or something?
There is a thread somewhere where we delve into this topic heavily. Someone claims it is a lazy autotuning job. I don't know enough about it to really have an opinion but yeah, someone dropped the ball.
The effect sounds also chorus-y. I really don't have an idea what happened in Chaos in Motion's post-production but the sound is horrible. I can't understand how Portnoy (and the other guys) agreed to put that out after the huge success that Score was. The bar was put way high, and they failed to deliver. I really don't know how the same guy (Kevin Shirley) that did the Live at Budokan, Falling into Infinity and Train of Thought mixes put out Chaos in Motion. *shrugs*
Now, I feel that LALP was DT's way of making that up (and with the funny LaBrie negating the existence of CiM thing and such) and putting the "DT is awesome live" flag. Regrettably, the whole thing was kind of underwhelming considering the huge amount of time taken to produce it.
With the JLB voice mixing thing, I agree with what rumborak said. Vocals in LALP sound compressed as hell, so the low breathing sound and hissing frequencies (listen to The Silent Man or The Spirit Carries On from that DVD) are at the same level than the powerful full-voice performances. I know compression is a standard in music production nowadays in basically everything (vocals being one of the departments where such processors are heavily implemented), but there's no point of comparison with Score's vocal sound. That's just pure bliss, it's perfect.