Yeah, right...The battery not charging always comes on when the filter is plugged...
In my '04 LB7, I was having a problem that took me a few weeks to diagnose, which ended up being a clogged fuel filter. The symptoms were very similar to this. When I really got into the accellerator pedal, the DIC would flash "Battery Not Charging", power locks would cycle locked->unlocked->locked, and the RPM would go crazy as the engine died out. If I pulled over and stopped, shut the key off, let sit for 5 minutes, and started back up, it was fine.
MY problem ended up being a clogged fuel filter. I don't know how this caused electrical problems, maybe it had something to do with the engine dying out with the truck going 75, and the alternator stopping suddenly stopping. I don't know if this is the same problem NoWake is having, but the symptoms sounded the same to me.
Replacing my fuel filter fixed my problem, and it hasn't happened since.