Re: J-custom RG8550 Vs Prestige RG2770. Why is the custom worth +$1,000?
Double check to make sure all nuts and bolts are tightly secured, especially at the neck joint and bridge. Like mentioned above, a saddle can be loose, or needs to be adjusted. So double check intonation as well, make sure it's dead on. Luckily, adjusting intonation is quick and easy with the edge zero. You could also try removing the ZPS system at the back if you have not yet, and also replacing the new stiff springs with older, more broken in springs. Also, if you haven't during your setup, install the locking studs and lube the knife edges with Chapstick.
I know what you're talking about in a sense. The 15th fret on the B string of my RG3120 rings out more like a harmonic for some reason and decays fairly quickly as well, unless I press a little harder than usual. It bugged me a bit, but wasn't a huge deal.. I just have to press a little harder if I'm going to ring it out.
I had an edge zero once with what I believe had a base plate issue. They are cheaper base plates than the previous gotoh made trems. If I used anything less than 10s, the low E and A saddles would vibrate, they had quite a bit of play in them, and I could hear it when doing palm mutes / half palm mutes. I swapped saddles around with the other strings, but no luck. Luckily for me, I don't mind 10s.
Lastly, what's the rest of your setup like? Do you have a noise gate? If so, have you tried with it off?