Take the car back to PepBoys and have them throw it on the tester machine, test the whole charging system. Also, how old is the battery? if it is older and 3 1/2 years I would think about that. Most won't give you more than 4 years.
You can get bad Alternators, I got a bad one (Bosch) from Pepboys last go around, in fact it blew all the charge fuses, they actually exploded in pieces, I suspect the Alternator rebuild house they get their alternators from put the wrong parts in or reversed the polarity... in any case I had to take the new one off and they gave me another new (rebuilt) and it was finally fixed, but had to replace the damned charging fuses as well. (those are huge amp fuses! .. they didn't go silently they exploded!)
