Thanks everyone for your input, I will try to respond to the questions asked:
1. As far as which strings are out the most I would say they are the B and G strings, which also bind in the nut by the way. I told the guitar shop about the binding the last time I brought it back and it was fine for a few days but they have started binding again.
2. Bender 4 Life - I tried your suggestions and you are right. I do tend to press hard on the strings and noticed the strings were either not going sharp or at least not going as sharp when I use a lighter touch. Man, it is going to be hard trying to unlearn something I have been doing for a long time.
3. Willy, I wouldn't trust my ability to change the nut myself, but I will ask about it when I bring it back to the shop again.
4. Ken, it's funny, but I was looking at Petersen strobe tuners on the Web shortly before I posted this thread. I see they are expensive, but it may save me money over the long run.
The strange thing is that the guitar sounds perfect when I get it back after the setups, but it then sounds off after a few days to a week of playing it. If the problem is the nut, or me pressing on the strings too hard, I would expect that the guitar would never sound in tune, but it does when the setups are first completed. Is there anything else on the guitar that would cause it to lose it's intonation in a short time frame?
I really do appreciate everyone's help, and the suggestion to not press so hard on the strings will help me even after I finally get this guitar sounding as it should.