So I just finished gluing my fret board on. Checked and filed all of the frets everything is level and true to form. All of the notes play right but when i put the capo on the 3rd fret and start playing, somewhere on the A string on the 12th fret it sounds high and a little bit muted but i can play the same riff without the capo on and the guitar sounds just fine
I don't know if I need to fix the nut, readjust the neck; the bridge or the tail piece but this is such a mystery to me. This is my first time attempting a re-fret job so I'm sure you can imagine my frustration.
Your intonation changes once you fret, because you've effectively shortened the scale length. You set intonation for the full scale length, but when you put that capo on, not only is it pulling the string slightly sharp by pressing down on the fret, but it's throwing your intonation out. Do you retune after you've put the capo on? That might help.