Unfortunately a lot of it comes down to timing and sheer dumb luck.
I was not admitted to any of the 7 schools I applied to during my first round of apps, and I had a 3.8+ GPA, 1500+ GRE score, strong LoRs, and a quite good SoP. This time around for Fall 2010 I was admitted to three programs, two at top schools, and one of those two within 24 hours of submitting my application materials (it was in the UK where they have rolling admissions, and I'd been in correspondence with the program director previously so he knew to expect my application and what my qualifications were). I did tweak my application a bit, including getting another LoR writer who could help target certain of my strengths better, but overall very little changed on my end between the first and second rounds.
What made the biggest difference for my second round of applications was that at one of the schools they had just launched a new MSc program that was a perfect fit for my research interests, which was relatively unknown, and which they were actively trying to recruit students for; at another of the schools (the one I eventually ended up attending) it was because the faculty member who became my advisor had reached a critical point in a certain research project (also a perfect fit for my research interests) which she wanted a dedicated grad student to work on. This new project hadn't been publicized until this year, so I would have had no way of knowing about it while putting together my applications, and because of the timing of it, if I had applied to this particular school the previous year, I might not have been admitted because I wouldn't have been needed as much as I was this year.
It's great that you have a strong application, but as in so many cases, at most top programs having strong numbers just qualifies you to be in the applicant pool. If you make that cut, the specific numbers are not so important. What makes them actively want to admit you is fit for the program, fit with faculty, and compatibility with their own ongoing research interests. Sure they want to take in the best of the best and give them a great education, but if they can afford to be selective (and most grad programs can be), they also want you to be a benefit to them, and to help them work on what they need to get done while in the process of acquiring that great education.