Yes, they do count. It's a careful dance. You want the Company to pay in as much as they are required. Then, if you calculate you are short and won't make the $51,000 limit, you contribute to your 401(k) on your own.
This is a high class problem. New hires won't need to figure this out for quite a few years.
I believe this is where we can make some significant improvements in C2015, while still not having to show 'Wall Street our (poker) hand.'