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I have a Behringer iAxe 393 strat clone.
I recently adjusted the truss rod to fix some frett buzzing.

Ever since, when tightening or loosening the strings while tuning, I sometimes get a creaking pop coming from the neck and the string I'm working on becomes a bit flatter or sharper. This sounds like it's coming from the truss rod.

What could be causing this?

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up vote 8 down vote accepted

If it happens at the same time as the string goes sharp or flat, it will be one of two things

  • slippage on the tuners, as @MatthewRead and @CornbreadNinja mentioned (you will be able to feel this if you hold a finger on the tuner while tightening or loosening the string - it will slightly jerk)
  • friction over the nut or string trees

I have had one guitar which had a nut friction problem, solved by rubbing a pencil lead into the grooves in the nut next time I restrung it.

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Dr. Mayhem has my vote on this one, I've been tuning guitars for over 4 decades and what the good dr. says is totally consistent with my experience. – filzilla Mar 22 '12 at 18:20
I had forgotten this but the notches in the nut had worn down and I filled them with superglue while I was adjusting the truss rod. This uneven texture is probably catching the string until its pulled tight enough to overcome the resistance. I'll find out when I get home. – Kalamane Mar 22 '12 at 21:43
Dr. Mayhem: it might also be that there's friction in the string trees, from what I can see the iAxe 393 has two of them. In my experience they can prohibit free movement of the strings (I prefer a staggered set of tuners instead). – morten Mar 23 '12 at 4:21
thanks @morten - updated – Dr Mayhem Mar 23 '12 at 13:29
The pencil lead Dr Mayhem suggests is actually a lubricant. If you've got another lubricant available safe for the materials, you can try that. I've used gun oil on a few bits of my equipment (away from the wood) to good results. – draeath Mar 26 '12 at 17:25

You may have over-tightened the truss rod. Have you tried turning it back slightly? That said, are you sure it isn't coming from the tuners?

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I'd expect it to be slippage on the tuners as well. – Matthew Read Mar 22 '12 at 16:16
When I read the question title, my brain played the sound of cello tuning pegs creaking. When I realized it was an electric guitar, it changed to the pre-climactic musical cranking of my old jack-in-the-box. – cornbread ninja Mar 22 '12 at 16:22

The squeaks are nothing to worry about. As the string is tightened, it travels through the nut. It sometimes squeaks a little, just like a tennis shoe squeaks on a floor. No biggie. If it really bothers you, next time you change the strings, put some graphite in the nut. It works as a lube.

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It could be coming from the neck... things to check

First loosen the strings and make sure that the neck screws (bolts in guitar terminology) are tight. Do not over tighten and make sure you use the proper size screwdrive so the screw heads don't strip. This is one place that could pop and creak.

Second the noise could be completely isolated from the truss rod adjustment - wound strings can pop if the nut slot is too small or tight - filing the nut should be done by someone with repair\setup experience as it cannot be reversed if cut to large or deep.

Note: I just saw your comment about the superglue in the nut slots... (after posting)

Truss rod, it's highly unlikely that even if the nut is stripped that the truss rod would repeatedly make noise - tuning a guitar is normally small increments (unless you are going between open tunings which require considerable tuning changes).

The truss channel is either under the fretboard (primarily Rosewood fretboards) or through the back (Skunk stripe) primarily on solid maple necks. If the truss rod has separated the neck it could creak - it should be visible from the side or back of the neck.

Hope this helps and good luck... you may need to have a tech or luthier look at it.

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