Same thing happened to me with Yale. I've submitted my requirements early, yet the online status check reported that I lacked recommendations. I called and e-mailed about it, and they said not to worry, because it's just very slow, with AMCAS and all. Up about late December, I got tired of checking and told my pre-med advisor to resend the documents. A few days later, it was complete.
Anyway, I have this feeling that they thought I wasn't up to their standards, so they paid less attention to my application than others (I knew someone volunteering with me who got his app complete rather quickly, presumably thanks to his 36 MCAT and Ivy league undergrad). I don't think the person on the phone even bothered to check my application. I want none of the volume excuse, after all, application fees more than make up for that.