I've never had problems with intonation before, but I noticed my guitar wasn't holding tune very well higher up the neck. So I do the usual setup, but the sound seems unaffected (I use the 12th fret harmonic method). So I detune the string and try again, and it doesn't work. Eventually, I've moved the saddle all the way to the back of the bridge and my string is still not proper.
(The fretted note is more flat than the harmonic note at the 12th fret)

This led me to believe it's a truss rod issue, but I'm not sure. I checked to see if the neck is warped, and I kind of think it is. I'm not sure though, because it is either a really shallow dip around the 12th fret, or it's me worrying too much and seeing things

Anyways, can someone start me out? I've been playing for 7 years, and I've never touched a truss rod in my life. Any help is appreciated.

Oh yeah, and stats. I'm playing an Ibanez GRG 06 LTD MK2... or what you need to know, it has a Wizard neck (I think Wizard II) and an OFR.

Thanks a lot UG
If your saddle is all the way back (as far away as the pickups as possible), you'll be flat. You'll want to go the other direction to raise the pitch.
Yea if you adjust your saddle forward it will have the effect of raising the pitch. you only need to touch your truss rod if your neck its warping or has a bend in it, sometimes to compensate for heavyer gauge strings as well, i had to tweak mine very slightly for my gauge 13's. try adjusting it forward in increments and depending on how far flat you are then if it is majorly flat move in a fairly decent amount, then move in small increments after that it may take alot of time to fix this but it's well worth it in the end.
Ill definatly try again before attempting to touch my neck, But I'm pretty sure I can't get it to stay in tune...
OMG Im a n00b. Sorry guys, the saddle IS closest to the nut. I was looking at it wrong. It is as close to the nut as it will go, but it is still flat.
I am starting to think that it is my neck. I'm not sure if you can tell by the low camera quality, but this is the neck:

If needed, I can take a higher res shot
you need a capo (or a friend) and mechanic's feeler gauges for this...

put the capo on the first fret of the Low E string (or have your friend hold it down)
hold down the last fret on the fretboard (21..22...24... whatever)
now use the feeler gauges to measure the distance between the string on the 7th fret

^note: some people use the 8th or 9th fret. Whatever seems more central on the neck to you.

It should be somewhere between .005" and .015" ... that means the neck is within spec.

If the neck is too flat, it will be less than .005" ... if to concave, it will be over .015"

if too flat, adjust the truss rod counter clockwise SLIGHTLY (no more than quarter turn) and let it sit for a an hour or two. Letting it sit will allow the neck to adjust and settle. Take your measurement again and continue the process until within spec.

if too concave, adjust the truss rod clockwise SLIGHTLY .... the same rules above still apply here.

Remember, even after the final measurement, the neck may move/adjust itself a little while it's settling in to the newly set tension (or lack of)... so expect it to change slightly (should be within spec though).

Do not make big changes in the truss rod. The measurement may be correct when you check it right after, but when the wood settles, it'll be way off (at the very least).

Once the truss rod is done being set, re-adjust string height, re-intonate, and you should be all set.

Hope this helps you out