I have the same exact problem with my wifes 99 Accord EX. I had the alternator replaced back in the summer, unfortunately I have gone through 2 more in the pas 5 months. The alternators were covered by the shop and they had a problemwith getting shotty ones. Well the alternator has been fine but the lights inside and out constantly pulse from normal to dim.

I even followed my wife as she drove it and the rear lights have the same problem. The check engine light is on (my honda dealer is no help) and the car runs perfect.

Any ideas aside from another alternator, they will not replace it unless it's dead and Honda is never helpful even though the car is still under warranty. I'mnotpaying another $80 for them to say it might be the alternator but untilit dies they can'tdo anything.