intonation problem

[Freekflag]

I just had my j45 set-up - brought down the saddle a bit. tweaked the nut. Nothing major. Basically lowering the action a bit.
Either I'm going crazy or the f#*$ing thing won't tune up.
I've tried the usual things.
It appears to be 'in' tune when I'm using an e-tuner.
However, to my ears something sounds "out".
Any suggestions before I call the guitar guy back?

[sliding-tom]

Can you give a couple more details what's wrong? Do you mean F# fucking or just fucking?

[Freekflag]

When I fret the G in a G chord it sounds sharp. The 6th e string always sounds sharp when fretted.

[sliding-tom]

Sounds to me like there is something wrong with the nuts slots, most likely not cut deep enough so your E and G strings go sharp when fretting them on the lower frets.

[Freekflag]

I meant the 6th e string fretted when doing a G chord but you may be right.
I did put some graphite in the nut slots. It sounded as though they were sticking a bit when tuning up.

[sliding-tom]

If any string makes a "squeaking" noise when tuning up it gets caught in the slot. If graphite helps, then you're O.K. Otherwise you will have to widen and/or polish the slot a bit. You can do that with a piece of guitar string and fine sandpaper (1200 grit) wrapped around it.

[Mandoron]

I would go back to the guy who set it up. I presume you paid for it? He shouldnt charge any more if it isnt right. If it is a nut hight problem it must be Way high!