I would do an octave chord on the 2nd fret A string and it would be in tune, then slide it up to the 10th fret or 12th fret, and it would sound awful and out of tune. For awhile I just thought I had a crappy guitar and thats all there was to it.
And then I found this video(s) when I bought my PRS, it changed my life:
http://www.youtube.com/watch?v=xV8kMUB8n4c
http://www.youtube.com/watch?v=-jfakcKV_2A&feature=related
Its the in's and out's of setting up a guitar that's fresh off the line. I did this to all my guitars, and I was one very happy guitarist.