Check a couple of things,
1) make sure the bridge is set really well, check the saddles and make sure you don't have one a little higher than the other. I had this happen and I had a dead string that would move that saddle up and down a little causing it to stop vibrating before all the others.
2) check you pickup spacing to the strings, I had my low E side too close one time after a set up and the magnetic on the pole slowed that big fat string.
3) check the first fret clearance, if it is too close to the fret it will slightly hit it causing a buzz and it will happen more and more up the neck you go. JackBass fixed his by going a little higher on the nut with some glue. With the tech tweaking the neck, he could have put a little more bow in the neck which eliminated the rattle, but the neck might have started to go flat again causing the rattle to come back a little later. Get something and stick it in the nut to lift the string and see what happens, if you notice the buzz goes away it sounds like you need to raise the nut a little. Many times you can take all the stings off, give a tap to the nut and it will come out, you can then add a little shim or some extra glue to lift that up a little. Just a thought to save you from getting a new nut cut.