
I turned the amp up, and it doesn't come through noticeably. I think it should be fine for now. I may even put the old saddles back on.
It could still be the nut. If the slots are too low, then the angle the string makes when fretted will be off. Try putting some thin (like 9's ) string pieces under each string to raise them a little off the nut and see if it persists.Definitely not the nut, because it does it when fretting almost exclusively. Also, the guitar is like 2 months old, so the frets show no wear. Frustrating, eh? Sad