I've been setting up my basses for the last three or so years. I've always had the G bridge saddle closest to the nut, then the D, then the A, then the E. Pretty common. Lately, I've been doing a lot of things to a bass that has required me to remove the strings and then put them back on and retune. One of the things I did was sand down the original nut. After I put the strings back on and setup my intonation, I noticed that the E bridge saddle had to be brought a lot closer to the nut, past the A and D saddles, and almost parallel with the G. I figured it was an issue with the sanded nut. Last weekend I did a crazy overall, repaired the finish on the body and the neck in a couple of places, shielded the cavities, changed pots, installed a thumbrest, moved the entire bridge a little closer towards the nut (because the G saddle was right at the end of the screw), and replaced the nut with and filed the new one. I am positive that the new nut is cut equally on all slots. Restrung and did intonation today and the E saddle is still past the A and D saddles. Could I just need a new set of strings? Anything else could be the culprit?