I agree that the problem is very likely the alternator. In fact, I would venture to say it is probably the voltage regulator, which is part of the alternator for your car. Take the alternator out and have it checked on the bench at Autozone or any big chain auto parts store that does free testing. Warning: if the problem is the voltage regulator, it may still pass the bench test. I had one E36 on which the weird lights blinking, etc., started happening only after the alternator warmed up, which you can't really reproduce on the bench at Autozone.
How long ago was teh alternator replaced? I would just go ahead and put in a new one.
P.S. (1) Your car has an inline 6 engine, not a V6. (2) There is no fuse for a car's alternator.