Just in case it hasn't been said enough...
Its your alternator. bought a brand new one because I was having problems. When I tested it on the car, with the headlighs, heater fan, four-ways, and dome light, t was putting out 12.9v when the four-ways were off, and 12.1v when on. When noting is on, I read 13.5v. I want to do some more testing, but I believe the stock 90amp alternator isn't adequate. If it is not in top shape, (which is what happened to mine), it's just too much strain on the charging system.