In the troubleshooting section of the manual it states that DC Current Offset at the amplifier outputs can cause a false reading.
I believe this is what was throwing things off.
In the guide it said to wire a 10uF 200v Capacitor inline with the grey wire to fix the DC Offset issue. (And I could find no other solutions on the net or otherwise.)
I managed to find a 10uF 50v Cap and it worked just fine. Problem solved, works perfectly, seems to be VERY accurate and VERY fast. Drops down to 0 INSTANTLY when I turn off the music as it should. The meter has this cool "Peak Save" effect, where it illuminates the highest peak, then slowly drops around 1 second at a time. This way you know if it ever hits the "Red" or "Danger Zone!"
I calibrated the Output Meter to turn to red at 49.5v.
The amp is rated at 49v.
I can now relax and enjoy the peace of mind that I have so desperately needed... I am way too OCD to spend $3,000, when I only make $8,000 a year, and not knowing if I'm pushing my system too hard.
Oh, and the cause of the DC Offset being a little higher may just be because I had (very unintentionally) abused my amp and had to have it sent into JL Audio for repair. I read somewhere else on the net that after an amp has been repaired it's normal for it to have a little higher DC Offset. Slightly harder on crappy subs, probably totally fine on my X12.
However, as we found out in this scenario, AC devices do not enjoy DC current and react to it violently even in small amounts.