Thats the nature of the beast. Sometimes if something goes, its not the part that went that was the original problem. Sometimes its something that made the part go belly up in the first place. Thankfully for you its only an annoying problem that isn't extremely expensive. I've heard other horror stories of people losing transmissions and just replacing them with new units, then finding out the new unit does the same thing not very long down the road because they failed to find the origin of the problem. At least its only an Alternator. I know this isn't extremely helpful, but try and consider the fact that you're driving a 16 year old vehicle and its bound to have things go wrong from time to time. Although they are nuisances, Your going to be hard pressed to find other vehicles of the same vintage without their own set of problems.
Think of it in a positive way to keep a cool head if you can. You are now positive, its not an Alternator problem and you can focus your efforts in different solutions. I personally haven't got a clue, but just wanted to post so that you don't just say, "F*** IT!" and sell it, go thru all that trouble and find something else with it's own bag of issues.
Good luck. Keep us posted if you track it down.