I bought a new alternator, put it on, same problem, took it off and exchanged it for another alternator, put it on, same problem. Unless I somehow got 2 bad alternators in addition to the one already on my truck, I'm thinking that isn't the problem.

Before I put my original alternator back on though, I did put some shielding around all the wires that run near it (aluminum foil wrapped with duct tape :rocking:), and the problem hasn't happened again yet, but I also disconnected the batteries and did an APPS reset at the same time, so only time will tell I guess.

Just so I'll know, where did you get the APPS noise isolator from and where does it hook up? Sounds like something you could make from radio shack.

You can get one from many places. it connects to the converter lock/unlock wire running to the pcm and the other end just grounds.

BD-Power Dodge APPS Noise Isolator

Awesome, so if it hooks up like that it has to just be a capacitor to 'soak up' the variations in the power supply. Some quick searching gave me this thread:

DIY: Noise isolator - Dodge Cummins Diesel Forum

Which says a $3 47uf capacitor from radioshack worked for him, does anyone with the $30 'official' version care to check or measure the capacitance of that one and share the info here? :D