It sounds to me as though you've got a guitar with a very active top: if the top were less active it would effect the sound less.
All guitars have a 'main top' resonance, and the issue is not so much what pitch it is at, as it is whether it's a problem for some reason. Unfortunately, it's difficult to alter the pitch of the main top resonance much without major surgery in most cases. The folks who have done controlled studies of this (see, in particular, Howard Wright's PhD thesis: "The Acoustics and Pschycoacoustics of the Guitar", given at the U/Wales in Cardiff in 1996. You can download it from their web site) seem to feel that the pitch itself doesn't matter a lot in the overall perception of the guitar's sound, within reason. Usually it's only the timbre of the notes close to the resonance that are effected, as you've noticed.
You might be able to spread out the top resonance, and weaken it a bit, by getting the back working with it. Usually getting the 'main back' tap tone fairly close to the 'main top' pitch will do the trick: I shoot for having the back a semitone higher (and sometimes even get it!). But if it's more than a third higher now any drop might help. Try adding some weight, such as a lump of poster adhesive to the back, which will lower it's pitch, and see if it has any beneficial effect. If it doesn't work, all you're out is the cost of the lump of goo.
If altering the pitch of the back doesn't work, parhaps reducing the activity of the top will. Again, you could add some weight, this time to the bridge. It will cut down the volume some, and possibly increase the sustain. See how little you can get away with to bring the problem under control.
These are only a couple of ideas, and the actual problem could be far different and require entirely different aproaches. In the end, internet diagnoses via ASCII text are not nearly as good as having the thing on the bench.
One of my 'test mule' guitars has a very strong 'main top' resonance just below the pitch of the open G string. When you play that string the top moves enough so that the fundamental of the note is actually split, showing up as two peaks in the spectrum about 6 Hz apart. If you listen you can hear the 6Hz beat frequency. Most people don't seem to notice unless I point it out, and, in some ways, it adds a little 'shimmer' to the sound. It's only a problem when it's a problem.