It was cut by someone with years of experience, and I had him size it for the set I'm using, .011-.054". He did screw up the first nut he cut for me on the 3rd string, but he did a second one for free. The second one didn't have any obvious problems, except that the 3rd, 2nd, and 1st seemed a little "tinny" but that was probably just because I was going from plastic to bone. He didn't set it up at all, only cut the nut, put it in, and strung it up to check his work.
I guess it started after that, I haven't done anything except change to a wound 3rd of the same size(the plain .022 3rd string had way higher tension than all the other strings, so it sounded a lot brighter) and I disassembled the guitar to polish the body and take a look at the neck pocket. I had a good look at the frets while the neck was off and they all seemed pretty uniform except for some scratches from the wound strings. Then I strung it back up, and set the action/intonation again.
Maybe the bigger strings just need more action. I'll try resetting it at 2.5mm. I don't remember what it was at before, but it was way up at 3mm after I put the neck back on.
Also, I tune 1 and a half steps low, they probably need more wiggle room that low. I haven't checked to see if it goes away at a higher tuning. I'll try Eb, at E they're like piano wire though. I'll do this first before I mess with the action.