Do you know that the rattle is coming from the truss rod? A loose tuner can cause a rattle that you could swear was coming from somewhere in the neck. I just had this problem on one of my guitars. Thought it was coming from the truss rod because of where it seemed the sound was coming from. I tried doing the same thing that packocrayons suggests above and it had no effect so it didn't seem to be the truss rod. Turned out to be a washer on one of the tuners that could move just enough to cause a rattle because the nut wasn't snugged all the way down against the washer.
If you haven't already, check the tuners thoroughly to make sure nothing is loose, including the tuner buttons. Packocrayons suggestion could be worth a try too.
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