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I think your pickups are probably too high. Check this out (from http://www.kinman.com/html/toneWorkshop/tone.htm):

STRAT-ITIS explained (Strat-itis = simultaneous multiple discordant frequency syndrome).

Dirty or rusty strings can also do this but many players know this horrible phenomena is caused by excessively strong magnets in the pickups, here's how it works. What happens is the magnets of the pickups pull a section of the string (the part that's over the pickups) into a U shaped vibration path. Normally the strings vibrate in what is essentially a single-plane path or pattern. Lets say that the time taken for a string (not subjected to excessive magnet pull) to complete one cycle or oscillation is X milliseconds. Traveling in a U shaped path it actually takes longer to complete one cycle or oscillation since the distance is greater via the U shaped path, so the time is X + Y milliseconds. Now it's getting clear that what you have is a string that has a section of it's length vibrating in a U shaped path and part of the remaining section raveling in a direct single-plane path and yet another section raveling at all frequencies between these two extremes. This means that the three sections are actually vibrating at many different frequencies when the string should be vibrating uniformly at a single frequency. What happens when you mix all these different frequencies together? Uggghhh, dissonant Strat-itis that's what! It's bad enough hearing 2 non-harmonious notes coming from a single string, but when you get multiple dissonant frequencies (or notes) being produced simultaneously from a single string the results are absolutely ghastly. A string that's out of tune with itself big time no less. That's what Strats do when you adjust the pickup magnets close to the strings. But when you adjust them to prevent Strat-itis, output, sensitivity and dynamic range are reduced and noise is increased when the Amp's Volume is turned up to compensate.
 
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