Only 1 of my 3 keys starts my car -- little help?

Well, as the subject says, I’ve recently found out that only one of my three keys will actually start and run my 2000 GTI. Weird, isn’t it? I tried to use my spare folding key last week, and I get “Immobilizer Activated” in the MFA with the blinking key icon in the tachometer. I also tried the valet key and had the same result. I then found my usual folding key, and the car started on the first try. I just tried both spare keys again last night, with the same results.
I know I’ve used all the keys to start and run the car at some point since I bought it, but since I’m the only driver of my car, I use one of the folding keys all the time, and the valet key and second folding key just stay in my desk drawer as spares (so they’re very rarely used – 1 or 2 times a year). What’s also odd is that all the buttons (lock/unlock/unlock trunk/panic) on the second folding key work perfectly, but the key won’t start the car. The only possible reason I can see for this is that I replaced the batteries in my everyday folding key. But I used the exact same type of batteries (CR1620, 3V) that were in there from the factory, so I don’t see how that could cause the problem I’m having, but who knows. I can't remember if my two spare keys have worked since I replaced the batteries.
I still have the key tag with the key/immobilizer code, which the manual says is required for ordering new keys and reprogramming the immobilizer. I’m just wondering if anyone else has had this happen, and what kind of money I might have to spend to get it fixed (I’m at 31.2k miles). From the manual, it seems like I would just need some key and immobilizer reprogramming, which seems like it should be painless and relatively inexpensive (but it is something the dealer would have to do, so you never know about cost). Maybe it’s possible to do this reprogramming with a VAG-COM? Any information would be greatly appreciated! Thanks in advance!