I am trying to adjust my intonation. Let me start with the facts:

All of my frets are flat progressively worse up the neck

the room in the saddles to
adjust forward to shorten the strings is not enough to compensate for this

My guitar is tuned to Eb

My relief measures about .5mm at the 12th fret when doing the "guitar string" test

there is 2mm between the bottom of my low E string and the fretboard - maybe 1 mm to the frets (at the nut)

action is 2mm at the 12th fret

Guitar is an RG321mh

I cannot for the life of me figure out why this problem is happening. I think the suspect may be either the nut or the relief, but I'm not sure. I posted in here because it seemed like a more obscure issue than the usual electric guitar setup-thread was for. Any advice would be greatly appreciated.
Anxiously Anticipating An Attractive ADA-MP1 Addition!