Depends on how you're doing the harmonic. If you're using the way described by Jimmi up top, just barely touching the string with your ring finger as you pick (the best way to do it IMO), then it will make a difference where you touch your right-hand ring finger to the string. The pitch and tone of the harmonic changes depending on where you touch the string (Satriani does a lot of cool effects with this). Try touching the string just above the humbucker, or if you don't have a humbucker, touch it in the middle, equi-distant from both pickups. This should give you the same note as the regular fretted one.