First time when you run a model in Accelerator mode, and have profiler on, the report also includes the build of the model into an executable (i.e., the MEXW64 file). Probably this is the reason you are witnessing high recorded time compared to actual simulation of the model.
One way to quickly check is, to re-run the model (which already has the accelerator mode file present modelName_acc.mexw64 in the path). This time the profiler will show lower recorded time.
Some of the other ways of improving Accelerator mode performance is captured here:
http://www.mathworks.com/help/releases/R2014b/simulink/ug/improve-acceleration-mode-performance.html
Thanks, Sandip
