I agree with Taylor that it is perfectly normal to have some 'dead(er) notes' on a guitar. This is due to a natural cancellation of the frequencies. There will also be some lively notes on a guitar due to additive frequencies. Due the physics associated with resonant frequencies, wave length, string diameter, fret board length... the dead notes tend to be in the lower register and the lively notes tend to be in the higher register. I was recently playing acoustically for some friends, whet up the fret board and one of them remarked that the guitar seemed amplified when I play up there. In most cases sustain and volume change of the dead and lively notes should be minor and only noticeable (if at all) to the player, but it can be severe. I want to mention there is a reason the same note say an E, 7th fret 5th string, can be dead while the same note on the 2nd fret 4th string does not seem to be dead, this is due to the length of the resonant section (the distance from the bridge to the fret of the note) of the string. This is also a common problem on electric bases. Changing the cancellation frequency(s) on a guitar is not easy. The best effort you can make is to have the guitar properly set up. I have actually sold guitars that I otherwise would have kept due to unacceptable (to me) dead notes. Good luck.
