I've had my SG special for five years now, from new. No matter how many times I've adjusted the intonation myself, taken it to the shop or changed the strings, the intonation on the third (G) string is out. It's immensely frustrating because its an otherwise beautiful guitar.
I've even recently changed the tune-o-matic bridge out for a graph-tech superbridge, but it's STILL out!
Has anyone had a similar problem? I'm running out of ideas!
Have you checked that the nut slot has been cut properly?
Also, what tuner are you using to set the intonation? I bought a Strobostomp a few months back and sold my Boss TU-2 because it didn't have the accuracy to set the intonation properly.