Try the intonation at various frets. A good way of doing this is to tune it accurately (a shop should have a tuner, or tune it however you usually do). And then try playing EADGB on each string and see how they match the open strings.

On the 'compensating for it' front, where you're living with a guitar with a known problem, try playing stuff with the capo in different positions. The intonation inaccuracies may show up more with certain chords in certain capo positions, so you can learn to avoid those situations when you play. I rarely capo at the 3rd fret on my main guitar - it's not miles out or anything, but it just sounds a bit icky to my ear, especially on C chords.

Graham.