I'm only saying "again" because I've posted a thread of the same name before...
Anyway, this is a slightly different situation: I recently decided to switch to a more "normal" string gauge (50-11s). After I put these strings on, I had to adjust all of the saddles toward the body (as they were all flat, for the most part), but for the most part, the strings are fine. My only problem is the D: I have the saddle set as far as it can go, and it's still flat (not deadly drastic, but it does sound pretty bad). Anyway, I don't really know what to do at this point. Can anyone help me out? In return, I've found Waldo for you...

Oh, and I have a Schecter Damien Elite, if that's of any importance
have you tried adjusting the truss rod?
my gear
amp: Marshall 200-Watt 4x12 w/ Fender FM100H
guitar: Ibanez RG4EXQM1 Quilted Maple Top Transparent Grey Burst
you may need to adjust your neck(truss rod). usually when you change string gauges you need to adjust your neck to keep the tension as it was because the different string gauges cause different tension on the neck and can effect the intonation. you shouldn't have to adjust the saddles too terribly much just little tension adjustment on the neck should do the trick.

However, dont just start adjusting away as you could seriously damage your neck. Do some proper research on the adjustment or take it to a tech. if anything he'll be able to fix all your possible intonation issues.
I don't understand why people are so afraid of the truss rod. It takes a hell of a lot to damage the neck with truss rod adjustments. Tweak away, just take it a quarter turn at a time.