some basses are problematic like that. I had a fender zone that came out of the box new like that, the E string always sounded dull like an old string. I tried anything I could think of (including the "witness points") and returned it to the dealer. They came up with nothing as well. I tried several different brands and gauges of strings. The dealer even contacted fender, who really offered no help. I ended up trading it back in and got something that sounded good (Schecter). I know that doesn't help fix your problem, but maybe it's time to let it be someone else's problem. Put a set of flatwounds on it and put it on Craigslist