UB Ed. Whistle Stop beat me to it, but the advice IS sound. The confusion may be caused by the interchangable use of the term "fret" for the fret wire and the space between fret wires. Sometimes however, a capo may impede hand positioning in the first position so a compromise can be made by backing the capo away from the fret wire or putting it on from the opposite side of the neck.
In any event, positioning the capo immediately behind the fret (wire) gives the best tone and intonation.
As for your guitar, it's likely not out of whack at all.
Good luck. Mooh.