some time ago i had my alternator go bad in my 03 gmc truck, and when i got a new one it was charging at 14.4 volts and the truck just didn't run right, and the battery light was still on. so you may be over charging you system and the computes don't like the extra voltage maybe. that's what i figured was wrong with my truck,

i returned the alt and replaced it again and it was running right again and the battery light went off. this one charged at 13.6.