For the past few months, I've been slowly realizing that the B string's intonation on my guitar (an ibanez rg w/ a edge iii) is pretty flat. So today i decided to get off my lazy arse and fix it, but I've run into a problem I have never had before.

The B string's intonation is so flat that moving the saddle all the way up to the tippy top of the bridge still results in a flat intonation. and yes, i did move the intonation screw to the upper hole.

I'm using Ernie Ball super slinkys .09-.42, the pink package, and the B string on my guitar is about 3 months old. Do you think replacing the string would compensate for some of the flat intonation (cause of string tension or something)? If not, any other suggestions?
have you tried not just adjusting the saddle but raising the bridge of the b-string? Can you even do that on an ibanez? I've done it before on my fender.
well your strings are a pretty light gauge so that might account for it. You are also supposed to change your strings pretty regularly, not just wait till they break, and when you change them, change the whole set. I dunno if that'll come through on helping with your intonation, but if not, it's just a suggestion to avoid other problems.
Just change your strings to see if that helps.
I once got a faulty A string and when I first put it on, the intonation was waaaaay off. I eventually replaced it again after I couldn't get the intonation right, and the new string turned out to be just fine.