I upgraded from Kali 2.0 Kali 2016 and after I logged in it would take almost 5 minutes of the gray screen before I was at the desktop. So I did a fresh install of Kali 2016 and all seemed well until I installed the Nvidia driver, version 352.79 and open CL, and the five minute delay to the desktop came back.
I could not find the cause but I did discover that if you hit the Esc key after the login it goes straight to the desktop almost immediately.
So it no longer is a major issue for me but a minor one now.