Sounds like the alternator is over-charging. You'll need to measure the voltages on the two small wires on the back of the alternator while the problem is occurring AND with the engine running.
You will find full battery voltage on one wire or terminal nut. The other wire is the key. It must be less but not 0 volts. If you find 0 volts, that wire going to the voltage regulator inside the Engine Computer is grounded, typically from being cut by a sharp metal bracket or laying on a hot exhaust part.
Normal on that second wire is 4 - 11 volts. The lower the voltage, the harder the alternator is working. If you find around 2 volts, suspect a shorted voltage regulator, but that is real uncommon. That circuit is pretty reliable. Because of other circuitry in the computer, a shorted regulator can not draw that voltage all the way down to 0 volts.
More likely you will find around 5 - 7 volts. That means the regulator is not defective but it is causing the alternator to work too hard. Suspect a break in the system voltage sensing wire going to the Engine Computer. That makes the regulator think system voltage is low and it will bump up the alternator's output.
Tuesday, January 3rd, 2012 AT 11:24 PM