Charging problem.

After lending my 1996 Isuzu Rodeo to my Brother in law, he left the lights on and killed the battery. We jump started the engine and as soon as the jumper cables were removed the engine died. We tried it again after attaching a volt meter and found that the alternator was not charging at all. I replaced the alternator with a new one and it still does not charge. I was told by the parts dealer that this alternator has an internal regulator and as long as there is power to it, it should charge. The battery has 11.5 volts and all fuses have been checked. The engine is a 3.6 liter V-6 and it has 163000 miles on it.