Atlas, MKL and OpenBLAS are CPU-level BLAS libraries, i.e. if you use GPU mode you do not use any of these libraries. The GPU-level BLAS package that is used by default is cublas and (if installed and compiled with) cuDNN.
I don't have the hardware to compare that timing to, but if you look at the reported reference timings (
http://caffe.berkeleyvision.org/performance_hardware.html), your performance does not look so bad. I'd say there is nothing wrong or to worry about with your setup.
Jan