I fought this problem when the AEM first came out for the Viper, and it took a bit to find what was causing the problem. Thankfully now the information is out there so others don't have to do the same.
There is a circuit on the car called "sensor ground". All of the engine sensors use this ground, and it goes through the PCM (or AEM) before going to actual chassis or battery ground. There is circuitry in there to prevent electrical noise from causing erroneous sensor readings.
Well, for some reason people running the VEC2 were being asked to "ground" this sensor ground directly to chassis ground. One of the favorite places (which made it fun to find) is the battery temp sensor back by the battery. Doing this bypasses the filtering ciruits in the PCM (or AEM) and is what created the problem. The AEM just seems to be more sensitive to this, and you will get all sorts of eratic behaviour. I have experienced the car cutting out with the windshield wipers cycle, headlights turn on, etc.
Anyway, hope that answers the question about this "mystery" problem.