Let's start by you listing each of the guitars that exhibit this problem, so we can see what they have in common.
I think the only thing they have in common are....strings!
But I also use different gauges on those guitars: 9-42 or 10-46.
I compared an assembled Strat (vintage bridge, hard rock maple neck, rosewood fretboard, 21 jumbo frets, single action truss rod), a cheap Kramer Baretta Special (vintage bridge, hard rock maple neck, rosewood fretboard, 22 jumbo frets, single action truss rod), 2 Ibanez RG (a recent RG655 and a 1991 RG570, Edge bridge, 5 pieces maple/walnut Super Wizard neck and rosewood fretboard on the 655, hard rock maple/rosewood Wizard neck/fretboard on the 570 with scarf headstock joint, 24 jumbo frets, single action truss rod), my Traverso Silky (custom made, long scale, locking Schaller/Floyd Rose bridge, maple/rosewood neck/fretboard, 24 Dunlop 6100 frets, double action truss rod) and my new Arrogantia (short scale, Schaller Vintage bridge, Schaller locking tuners, zero fret, quartersawn maple/ebony neck/fretboard, 12 jumbo + 12 narrow jumbo Jescar EVO Gold frets, double action steel truss rod).
The funny thing is that the only one of the aboves that seems to have not the issue with dead spot on the G string at 12th fret is the Kramer....and the one that shows it more is the last Arrogantia.
The other guitars stay in the middle...being worst than the Baretta and slightly better than the Arrogantia.
In any case, G string's sustain at 12th fret seems to have less sustain than other strings at the same fret or the same string at other frets in most of the cases.
On the Arrogantia I improved the situation with the following actions:
1) light frets sanding and polishing (now they really shine!)
2) better truss rod adjustment and neck relief
3) complete new setup with 9.5-44 strings
The dead spot is still there, but there's a little more sustain and a more natural decay.
I did not attempt to fix the issue on other guitars yet.
Now I've to verify what happens with my SG Standard and 1987 PRS Custom (these are known for having a lot of dead spots here and there all along the fretboard...maybe due to brazilian rosewood?).
By the way, this is something I can live with and forget.
When I bend the G string at 12th fret it sustains excellently and when I play the note it sustains enough to create not any real problem.
I assume Gale Frudua is right when he says that this is the nature of wood and instruments.
I'm just curious to see what will happen in the next years with neck's stabilization and woods seasoning and drying.
I also cannot tell if that frequencies are "killed" by maple or ebony...but I'm thinking about ebony, since all other guitars have rosewood fretboars...
Maybe that ebony have a particular density around 12th fret's area, who knows?