Actually, first thing is three stupid questions. First stupid question: have you changed the strings since you bought it? Old strings will be dodgy intonation-wise. Second stupid question: you are tuning to concert pitch EADGBE, aren't you? Dropped tunings will generally give you grief on intonation. Third stupid question: you're not leaning too hard on that bottom E, are you? Some players (especially the wrap-the-thumb-around-the-neck school of folk guitar) can grip the strings tighter than necessary and essentially put a slight bend on every fretted note. Hopefully they're stupid questions, but ruling out "user error" is always worthwhile.
Also check humidity in your house. If it's *very* dry air then this can be a problem as the wood shrinks. I've not personally found it a problem, but then the UK generally has a fairly moist climate, and a combination of drying clothes and damp dogs tends to keep our place fairly well humidified too. YMMV, especially if you're in the States.
Assuming the intonation is still duff though, take it back to the shop and don't try to sort it yourself. If the action at higher frets is a bit high too, it's probably just a truss rod tweak, but it's not impossible for it to be something more serious. I know most shops don't have enough margin to do a full setup on everything that passes through their hands, so most instruments will just be shipped as they come from the factory. So you don't want to mess with it yourself, else the shop will (rightly!) tell you that they can't return/fix it after you've buggered about with it.