I've seen it with heavy strings before on many guitars, not just the Jag-Stang. Might need to lighten the string gauge. The Low E is the biggest B**** to intonate IMHO b/c of this problem regardless of the guitar. Gaaah, having bad flashbacks to my .014 gauge string days.
Also, you could maybe compensate by moving the whole bridge back a little bit too, the bridge freely rocks in those two little thimble things in the body. Could be you have it pushed all the way toward the neck. I have almost spotless intonation on mine but I'm also running .009's and have the bridge centered.