A follow up on my previous comment:
I was really curious to see what is going on. I can confirm that I do get a lower sustain around the 12th fret of the G string on the following guitars I own:
- EBMM JP-6 2015
- Gibson Explorer Traditional 2016
- ESP James Hetfield Signature Truckster 2006
- Ibanez Iron Label 7 string 2014 (this one's the worst -- I get low sustain everywhere)
Notice that all these instruments are vastly different from one another in terms of wood, construction, hardware, pickups, and age. Your observation is very accurate. You tend to get lower sustain on the 12th fret of the G string, and quick transition from the fundamental frequency to the harmonic overtones past the 12th fret. This is more of a physics phenomenon, and is why the laws of universe keep things together the way they are. As your string length decreases, your fundamental frequency becomes weaker in terms of amplitude and instead, it is the overtones that cause the sound to sustain. Try plucking the strings on the headstock, and you can definitely hear the difference.
The rule I came up with is this:
- Longer string sustain > shorter string sustain
- Thicker string sustain > thinner string sustain
- Thick long string sustain > thick short string sustain
- Thin long string sustain > thin short string sustain
- Thick short string sustain > thin short string sustain
- Thin long string sustain > thick short string sustain
These rules only hold in a perfect world, where there are no frets, no fretboard, no magnetic pull from the pickups, and no unintentional and subconscious change of picking style, angle, and force when moving to strings of different thickness.
On the other hand, the guitar is a very inaccurate instrument, because of the way it is constructed. You never get perfect intonation on a guitar that has the western equal temperament fret system. That is why a lot of people are fed up with this, go crazy, and resort to true temperament system (which to my ears sounds out of tune -- due to many years of western music equal temperament ear training). Hence, it is natural for you to get lower sustain and more harmonics on certain notes on the guitar.
Now, with the above observation in mind, the Petrucci guitar is an extremely precise instrument, in that, it will show the slightest of these inaccuracies both in the guitar itself and from your playing style. That's why EBMM charges such a dear price for these guitars. Also, bear in mind that your EBMM guitar is an alive creature. It will change, it will get better as it ages and the wood dries (or could get drastically worse, depending on your maintenance standards); it is almost certainly going to need more attention compared to some mass produced instruments. And that is a good thing, because you know the more care you put into your instrument, it's going to love you back even more. Although, the Petrucci line has stood the test of time, both with Petrucci himself using them, and thousands of Petrucci fans playing these guitars, including myself. I recently bought one, and had a few problems myself. But the benefits of this guitar far outweigh the small issues.
In summary, I suggest to bear all these points in mind, and spend a little bit of time working around the issue. I know you live far from the EBMM factory, so it might not be very convenient for you to send your guitar to the factory. So perhaps, you can just alleviate the problem with regards to the points in my previous post, and also learn to live with it with regards to this current post.
Good luck, and enjoy your gorgeous new guitar!