Hey, I've been having awful intonation problems, and I can't seem to figure out what's going on. This is for a Cort Zenox Z44 special edition I have tuned to drop B with .60 - .12
So first off (intonation has always been off), I have major buzzing from the big string rattling on the next fret over. My initial though is to add relief to the neck. I did, and the buzzing went away. But, this made the strings high enough off the fret board that intonation was worse then it was in the first place (which was pretty bad). So I lowered the bridge to even it out a bit, which helped a tad. The fretted 12 fret note was about a quarter of a half step sharper then the actual harmonic, the lower notes were sharper, but the higher frets were extremely flat. I've adjusted the bridge to as far as the screw will allow, and the 12 fret is closer, but the frets before are still a massive amount sharper, and the higher notes are still insanely flat. No matter how close the 12th fret is to the open note and harmonic, this issue ALWAYS persists. I removed some relief, but now the buzzing is back. Like seriously, if I fret the 6th note on the big B, it's flat against the 8th fret. My only other thought is the NUT! The guitar was originally made for standard, (I assume), which makes me assume the nut might be too low to the fretboard. No matter what I do to the action and intonation, nothing works properly. I need to add action, which I can't do without making the notes much more sharper or flatter then they are in the first place! 
It has a standard tunomatic bridge, no locking tuners or locking nut.
Actual measurements would help considerably.

Pictures at least.
Ibanez RG1570 Prestige
Jackson Kelly KE3 - MIJ (Distortion/Jazz)
Jackson DKMGT Dinky (EMG 81/85)
ESP E-II Eclipse Custom (JB/'59)
ESP LTD EC-1001FR (EMG 81/60)
Fender MIM Strat

Mesa/Boogie Dual Rectifier Roadster 212
Laney IronHeart IRT-Studio
Peavey Vypyr 30
Peavey ReValver Amp Sims
TOOOO many T.C. Electronic Pedals. . .