Like the title reveals I had my axe plek’d and the nut replaced. The guitar won’t intonate on all strings. I already changed strings. Didn’t help. Current stings are NYXL 10-46. Pick ups are at a reasonable height at 5/64th and 6/64th respectively. The weird thing is the 12th fret harmonics are all on point but the fretted notes aren’t. They’re all flat about 8-13 cents. I can adjust the saddles either way it never changes. It stays flat. So the guitar doesn’t respond to my input. I’ve never had this issue on all strings. Usually it’s a bad string. But like I said I changed strings already and that didn’t help. It’s not a bad batch because I use the same strings on other guitars with no issues. Same batch. I’m at my wits end. Either they messed up the plek job or the nut isn’t cut right. I will mention, though, that I had to other guitars pleked and they don’t have that issue. Maybe I got lucky, I don’t know. Any idea what the issue could be?