There is probably no way to record it, but I will try today so you can hopefully hear what I am referring to.

In the mean time I will attempt to explain this.

After I am all tuned up (Yes, it is perfectly intonated as well) and I play either the G and B strings open together, or the B and E strings open together, or all three at the same time open, I can hear this ringing sound. When I mute out one of the strings after striking them together, the ringing stops. If I had to guess, I would say it is the B string causing this issue, but I can not figure out why it is doind this.

It also does this when fretting chords like a D or C, but the ringing is not nearly as noticable. I think this is just because there are a few more sounds ringing out to cover up some of the problematic ringing I am talking about.

It does not seem to be the nut, the bridge, the saddle, or the neck/frets.

Could having a battery in the same housing that the pots are in cause this to happen? Could the pick up's be causing this? The pick up height maybe?

Thank you for your time.
It's not how you pick your nose ... It's where you put the booger!

im pretty sure your guitar is resonating, mine does it too
Bands I've seen:
Lamb of God
A Day To Remember
In The Walls
Saints Alight
Live As A Monster
Bleach The Skies
Red Ribbon Army
The Amity Affliction
Buried In Verona
I figured that much. I was just wondering if there is a way to filter it out, or make it less noticable.

My fender strat does not do it to the extent my two Epiphones are doing it, and acoustics do not seem to do this at all.

Do EMG pick up's make this issue worse for some reason?
It's not how you pick your nose ... It's where you put the booger!