You should be able to call Apple and provide them with your proof of purchase to get your full warranty. People do it all the time with iPods if they forget to register them. UNLESS, the only way you are going to have a problem is if:
Customer bought MacBook from Best Buy.
MacBook died a few months later..
Customer caused a stink and Best Buy just replaced the MacBook for the customer, even though it was out of the DOA period.
Best Buy now has a broken MacBook, and they get it "refurbished" from Apple, and are trying to sell it as new.
Now, this may not be the case at all, but really it's one of the only valid reason I can see your warranty not being 1 year...or like Tracey said, they returned it a few months later just because...
Either way, Best Buy knows FULL well why you aren't getting your warranty, unless they really just don't know what they are doing, which I deem highly unlikely since they are seling Apple computers everywheres...Or the employees are just really dumb. But if they are compensating your financially, then I'm sure a little less warranty will be worth it.
Tell them to sell you AppleCare at their cost