I had a variety of similar problems in my Jeep (2000 Wrangler) using the factory wiring harness. I wired the empegs constant lead directly to the battery as someone else suggested and haven't had any problems since. It also cured a pesky alternator whine sound that I was never able to completely get rid of before. Just use 12 gage or so wire and be sure to put a fuse as close as possible to the battery in case something shorts out. You may also want to bypass the harness ground. I grounded to the metal frame supporting the dash more or less right behind the empeg which has worked fine so far.

-Mike