Thanks for the intonation lesson Dr. Simon. I played with the saddle adjustment and I am staying in tune much better now. I have always been shy about working on guitars, except for re-stringing, but electrics seem to be easier to make simple adjustments.
I have another problem. I can't get much volumn out of the high E string. No matter what the setting I get a thin, week sound from that string. Not much sustain. How can I make that thicker and fuller? I am using the factory single-coil pickups that came with my Strat.