My car used to have that problem also, I replaced both the voltage regulator and put in a new 100 amp alternator and the problem was solved. I did both at the same time so I still don't know which one was the culprit.

 

Well the OP didn't really tell us much such as what kind of alternator he currently has. Or if the lights were pulsating at high RPMs such as on the freeway or just idling at a stop light.

OP you coming back man?