I am running Ubuntu Mate 15.04 on my machine. I have had issues for the past year running different Ubuntu derivates. The issue was that every time I wanted to shutdown or restart, my system decided to halt. So, what I did was search for a solution (rather unsuccessfully.) For all who suffer from the same problem. Here is how to get rid of the issue:
Go to the BIOS settings (press Esc during boot)
Change the USB3 setting (you will find it in pre-OS option) from “automatic” to “enabled”
That’s it. From now on restart, shutdown, and suspend should work as it should.