Er, well have you checked you intonation to see if it's correct? If it's a litle off and the action is set high, using a capo will put it out of tune. For example i have one guitar tuned to open D with heavy flatwound strings that i use for slide. The intonation is correct but if i use a capo on the 4th fret i have to retune the two top strings cause the capo pulls them down and out of tune in relation to the lighter strings.