Does the low E go sharp when capoed?
Does the low E go sharp when fretted at three or five?
If both are the case, it is related to the guitar.
If it only goes sharp when capoed, it is related to the capo.
If both happen, is your action high? High action will go out whack when fretted. Low action won't.
There is more to say and consider. But, first, determine if it is a matter of sharpness and if it only happens when you capo or if fretting will do the same thing.
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Paul
-You could just as well be hung for a sheep as a goat.
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