This problem actually exists on MOST guitars, to some degree. Equal tempered tuning isn't accurate. The first few frets of most guitars actually are slightly sharp. Look into the Buzz Feiten tuning system - it talks about this.
Basically, guitars with a straight nut cannot intonate perfectly across the fretboard. Our ears generally don't notice things being off. Sadly, mine do, and this drives me kinda crazy.
I have my gripes with equal temperament too, but I don't know if that's the problem here. I'm guessing that sockwalker has played other guitars and that most equal-tempered guitars sound "in-tune" to him. (We all know they play every interval out of tune except octaves.) But equal temperament is generally close enough for most people, and something else is wrong with this guitar, otherwise he wouldn't have noticed a problem. For most people to notice something being "out of tune", it must be seriously out of tune, and the tuning inaccuracies of equal temperament are generally small enough that most people don't notice them.
Also I think he was using a tuner rather than his ear. I'm pretty sure that tuner would be set up for equal temperament, not just intonation or another system. So if the tuner says it's out of tune, it's out of tune with equal temperament. An equal tempered guitar is the goal here, since it has a normal nut and straight frets.
Ok, I wasn't fully clear.
Guitars are OUT OF TUNE with equal temperment. The strings are different widths and press down different amounts depending on where you are on the fretboard AND that tension is spread across the string differently as you go from the nut toward teh bridge. Pick up a few guitars and put them through a tuner and you will see that even an "in tune" guitar can be out of tune as he is describing.
The easy answer is to move the nut forward a bit, as this helps balance things out.
