alright, so I just got a used guitar, Jackson Dominion.
I use 9s - 46s (light tops, reg. bottoms)
I own 3 other guitars and use the same gauge strings, but they have used that gauge for years.
the previous owner used much thicker stings, 13s or something, but he tuned way down.

my other guitars have perfect intonation all over the fret board.
On the jackson I had reset the truss rod, the action and it plays perfect, near 0 fret-buzz, but I just cant seem to hit perfect pitch for the bottom three strings.
when you look at the bridge saddles on my tune-o-matic for those strings, 4th and 5th is pushed way back, and 6th its pushed way up and eventhough each string is intonated at 12th fret, when i go up the frets, the intonation totally goes out of whack.

so right now, I have the saddles set where they look right, hoping that the guitar somehow gets used to it or something, as you can see, I am losing my mind.

what should i do?

(i dont want ppl saying "what did you get a used guitar!" or "jacksons suck!")