Are you sure you are complete? Did you get a complete email? 'cause I thought I was since the end of August, then I found out that they were missing a part of my application (which I sent but they apparently never received!!)and never bothered to let me know! Good thing I decided to call to find out what was going on.
I had this problem as well. Columbia was one of the very first secondaries that I received (in July), and I had it finished and ready to go less than two weeks later. I had my letters sent from two different sources, one of them being Interfolio.com (which manages my grad school refs). On Interfolio.com, certain schools have an "electronic delivery" option which, in my opinion, is more efficient than regular delivery. Plus it's a dollar cheaper (which doesn't add up to much, but still, money is money). Anyway, I selected this option. Columbia would now have all of my materials. I received what I believed to be a confirmation of completion email, and I settled down to wait patiently.
Fast forward to mid-October. (Note: Nearly THREE MONTHS LATER). I get an email from Columbia's OoA, alerting me to the fact that my application is still incomplete, pending my letters of recommendation. I freaked. I called the office, and apparently they had never received my Interfolio documents. You see, Columbia doesn't accept electronic deliveries. It boggles my mind as to how it was even an option on the Interfolio site (it should only appear as an option for schools that accept them). After a lengthy conversation with Interfolio and Columbia OoA, Interfolio agreed to refund my money and overnight my file. However, this was little consolation, as I was now complete THREE MONTHS after my initial date of submission. I don't know if this will end up affecting my chances of admission, but I'm sure that it won't help. (It turns out that the "confirmation" email that I had received was for the online secondary submission, and was not a "complete" notification.)
Moral of the story: MAKE ABSOLUTE SURE that they have all of your supporting documents, especially if you are using Interfolio. You obviously cannot count on the schools to let you know if your application is complete. Perhaps this is why they keep sending out those "complete your secondary" emails? The lady that I spoke to at the OoA did mention that I was not the only person that this had happened to.