I've read a lot of posts where folks mentioned the stock nuts on Gibsons not really being too well made, causing problems, etc. Consensus seems to be that tuning problems are most likely caused by improperly cut or angled string slots.
Re: nut making no difference to fretted notes - this is one of those endless bone (so to speak) of contention type issues that is completely polarized after being rehashed 1000+ times on guitar forums. I find it quite interesting that for every person forwarding the very logical argument that once a note is fretted the nut is out of the picture, there's another who firmly believes that despite such a logical argument, a new nut made of some different material than the original changed the whole tone of their guitar, fretted note or open string.
I'm with the latter group. New bone nut on my Epi Standard made the whole guitar sound better, IMO. Wished I'd kept the original bone nut on my ol' 69 SG, when I got the brass one put on the whole tone of the guitar changed and I was never really as happy with it. Of course, it still sounded great, but was subtly but definitely different. How can this be explained? It can't, it's not logical, but I know what my ears tell me.
Kinda like the old TonePros bridge/tailpiece debate really - some hear a difference, some don't, some say the strings don't vibrate past the string saddles enough to matter, some do. YMMV as we say on the intrawebs
