I have had this problem before. Happened on my open E, A and D strings. But not when they were fretted. At first, I also thought that it might be my truss rod, or any number of other problems. For me, though, it was because of the string size that I was using. My nut is cut for a .045-.105 set with a .065 and a .085. I noticed the buzzing sound after I put on a new set of strings. By process of elimination, I found out that it was not coming from any of the frets, nor was it the bridge, or even the tuners (all were in excellent condition). I then noticed that the strings that I had strung with were a .045 to .100 set with a .060 and an .080. The quick (ghetto) remedy was to stick a small piece of tissue under the strings so that they did not rattle around in the nut. Unfortunately, my nut is a graph tech which is black. So you could easily notice these weird white things stuck under the strings. Not a pretty sight. I might suggest that you ensure that everything on your bass is tightened correctly, that your neck is straight, and then check and see if you are having the same problem. The nut will eventually be worn out, especially if you do a lot of bending (I love to bend my notes) or change your strings often. It might be time for a new nut. Hope this helps you a little bit!
