^ plug in to a decent tuner and crack out a harmonic, if its flat, check the intonation.
Yeah, it's most likely your intonation.
Here's what you do..
1. Get a good tuner.
2. Play the 12th fret harmonic. It should be in tune.
3. Play the 12th fret note, actually fretted. If it is in tune, than the intonation is correct.

Do this for all strings.

At least, that's what this book told me to do.
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