The only way changing the nut should change the intonation is if it isn't fitted back in the same place as the original (i.e. if there is a gap at the end of the fingerboard, or if cleaning out the slot from the old nut you took out fingerboard wood), or if the action is very high at the nut, and even then you should be able to get the octave harmonic in. When I fit nuts I use a set of feeler gauges and a set of nut files to set the depth. You need to check the fret height really to set the nut up properly. It will vary from guitar to guitar because of this.
However you say it wasn't correct in the first place, which smacks at something else. Did you measure the scale length? As a rough approximation, the distance from the nut to 12th fret should be the same as the distance from the 12th fret to the bridge. I say a rough approximation because the bridge on a Les Paul is slanted to give more length to the bass strings. If you can't adjust the G string to this length, then that will be your problem. The only other thing I can think of is the gauge of strings you are using, but they would have to be quite extreme not to intonate.
