Need help intonating ibanez artcore

[BoRadBass]

Just got a Ibanez AGB140 used. It needed some adjustment and new strings. So I strung it up with some rotosound flats,tuned it, adjusted the truss rod, then set up the action. All went well until I went to adjust the intonation. The problem is that I can get the "A" and "D" strings to intonate perfect, but the "E" and "G" strings stay flat at the 12 fret no matter how much I move the saddles, however it does effect the tuning and the sting tension. It has the gibralter III bridge ans stop tailpiece. I have tried allot of different thing to address this including raising and lowering the action, raising and lowering the tailpiece, and moving the saddles to both extremes. I am almost on the verge of giving up and bringing it to my local shop and paying!!! Any help is greatly appreciated.... Thanks