From Peace: "It's a guitar tuned low."
What does this mean? Is the open-string tuning at lower pitches than the standard EADGBE? (A friend of mine does this, to where he has to capo on the 2nd fret and play C forms to match a normally tuned guitar playing C forms open. It lets him use C forms to play in B [capoed 1 fret] or Bb [open].) If this is the case, and particularly if you're not using lighter string gauges to compensate for it, I would supect that the strings are slacker than they're designed to be, and that they would more readily distort when fretted. This could make your intonation significantly off.