Keep in mind that Sean's 1000W amp is only going to be 3db louder than a 500W amp and 6db louder than a 250W amp. He may also be using high end component speakers which sound great, but have a lower SPL and need the extra power. Don't assume that high wattage = earthquake force sound.

Now to get back on track of Sean's original post; good greif -140A!!! . I am assuming that is peak power and since these are McIntosh amps they have clipping protection that shuts them down momentarly if they exceed their rated power. As someone who's done multiple amp systems for the past 15 years, I'd first check your alternator's specs and find out what continous current it is capable of supplying. I've had to upgrade to higher current alternators in the past. Rob is correct about the high current capacitors and that would be my next suggestion. It sounds like your cap is working fine, but it may be robbing your other devices of current. Go to an empty grocery store parking lot with your fluke DVM and monitor the voltage to the empeg unit. Most Fluke DVMs have a analog LCD meter below the digital readout that is updated more frequently than the digit display and simulates an analog meter just fine. While the engine is idling, turn on your high beam lights, wipers, rear window defroster, seat heaters (if you have them) and vent fans on high. Add anything else that you can think of that will exercise your alternator. Next put on some Drum&Bass, Trip Hop, or 1812 Overture with the cannons or anything else that will exercise your subs. See if you can duplicate the problem while parked and see what the voltage drops to. This should give you an idea of whether you simply need to add a cap to the empeg power line or do an alternator upgrade.

Let us know how it worked out for you.
Cheers!
Dave