when i bought my first HO alt, it worked good for a minute then the regulator went out. i didnt suspect that was the prob, but after testing everything else realized that was the prob, got a bew one and all was fine...
your problem is very easy to diagnose... somewhere in your electrical setup and wiring, you have done something wrong or you are having equipment failure at the batt or alt level. Plain and simple, unless you have some crazy issue such as exposed wires grounding out a bit or dumping part of your voltage to part of your car.