Well, I was recently learning the tapping part to The Forgotten by Joe Satriani, and I realized that the sound was completely off. If I play the notes normally, it sounds as it should, but when I tap it, the sound is completely off, more of a mix of a very low sound and a very high sound.
What could be wrong here, intonation, something else? I'm a n00b when it comes to problems on my guitar.
I don't need a sig....
were you playing through an amp or not? if you arent playing through and amp and you tap you get the notes from both sides of the fret
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Yeah, if you're not playing through an amp, you're getting sound from both sides of the fret, so if that's the problem, then just plug in to an amp.

My things:
Bowes SLx7
Washburn WG587
Washburn X40Pro
Washburn X50
Washburn HM24
Washburn WR150
Laguna LE200s
Arietta Acoustic
First Act
Valveking 112
VHT Deliverance

How do normal hammer-ons and pull-offs sound (without picking just doing left hand legato)?

If they sound ok you may need to develop calluses on your tapping finger/s because soft skin on the finger tips can actually mute the sound. Try tapping using your pick everytime the right hand taps; if it sounds ok that way I bet it is the callus needing to be built up.
maybe he uses a whammy pedal??

that could explain the mix of very low and very high sounds..

i havent heard the song...