Hey gang,
I tune the open string, then do the harmonic at the 12th fret, then note at the 12th fret. Depending on that note I either lengthen, or shorten the distance. All of my guitars are dead on, with all 3 notes. It's a little harder to check that way, but that's what works best for me. One other thing I lay the guitar in my lap, so that all the pressure is off the neck. I've never been able to set the intonation accurately holding the guitar upright.

I do alot of stuff with guitars with the exception of fret work, and the electronics, not what I would like to be with a soldering iron. I had a set up to do for a guy who's wife works with mine, and he wanted really heavy strings on it. The neck on this cheap copy of a strat was not built to take it, really the guitar was not built to take it. Anyway, I put the strings on it like he asked, and tried to set the intonation. It was next to impossible, and I got it as close as I could. I just couldn't pull the saddles far enough back to get it right on the heavier strings.

I know there are alot of players that use heavy guage strings, but they make some modifications to the guitar so it can handle it. You can't just go buy a guitar, and put a heavy guage set of strings on it. Your action is going to be high, and you probably won't be able to set the intonation. If you want to play heavy guage strings, take the guitar to a tech. Have him tell you what you need to do to use heavy guage strings.

The reason I posted this is the problem sounds really similar to what I was going through while trying to set up that guitar. I didn't even charge him to do it, he finally came back a couple of weeks later and asked me to put a set of light guage on. I did, and set the action, then the intonation perfectly for him. It made all the difference in the world on that guitar, but all guitars are different. This may not work on yours, but give it a shot if you happen to be using heavy guage strings.