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Strange harmonics on A string

I was recording some tracks last night when the drummer commented that the A string seemed to have a different sound than the E string. After playing the different strings, it seems the A has a ringing harmonic that the others don't have. Any ideas on how to dial this out? I believe the bass is intonated correctly, but could that be related to the problem? And yeah, I know it isn't wise to listen to a drummers opinion, but he was actually on to something this time!
 
The A string on Fender-style head often has this problem because there is not enough downwards pressure as the string passes over the nut. The G and D strings have the string T holding them down, and the E tuner is closer to the nut. Make sure that the A has enough wraps around the tuner post to keep the string down.