Alright so when i'm playin my Ibanez cayman unplugged from my amp some of the string sound off, but when i put them to my tuner, which is the kind that clips onto the headstock, it still says the tune's dead on. could this be because since its an unplugged electric its not as loud sounding so the tuner can't get an accurate reading? if so how can this be solved?
it's most likely an intonation problem

Gibson Les Paul Standard
Fender American Strat
Taylor 214ce
Mesa Boogie Triple Rectifier (about to be Voodoo Modded)
Keeley TS-808
Boss GT-10 Processor
Boss RC-20xl
you could tune and then go to www.tunemybass.com and compare. if its off you could get an electric tuner. i thought the headstock tuners are built for acoustics, but maybe not. i thought they were suspoced to be pretty accurate.