The tolerances are so tight that I can imagine a situation where it looks fine, but it really isn't.

As an example my LP Standard developed some really nasty fret buzz on the high E string when played open. It was rattling on the first fret! I had never really looked at the nut closely before, but to my untrained eye it looked like it was cut way too low. Logically, I figured it had to be a setup issue since it wasn't like this to start with.

A tweak of the truss rod 1/4 turn fixed the problem. The nut was fine. The amount of distance changed at the first fret was probably not even measurable, yet it fixed the problem.

My point is this - even though everything may *look* OK, a setup adjustment may very well take care of it.

Something just struck me now that I should have suggested before - put a capo on the first fret and see if the problem goes away or changes. Doing that takes the nut out of the equation. Something to keep in mind for the future.