Reboot doesn't always work

I recently put together a new machine and it has started to be a pain.
The Hardware is GA Z97X G3 M/B, 32gb 1600mhz Ram, G3258 CPU (new), Samsung 840 EVO 250gb, 750W Thermaltake PSU and 2 GTX 660Ti.

When I first installed everything it worked FINE and I had no issues what so ever but, I recently added my 2 extra HDD's and it still functioned ok but, from time to time, when a NEW install happens, I go to restart the machine and it goes to restart then just sits there, there are fans going and lights come on but, nothing. The monitor shuts off and the keyboard goes off but it doesn't restart. I have to force close it down and restart and it boots with no issues.
I did have a similar problem after I had installed Roxio where the machine would not shut down but I stopped a dll from loading that wasn't needed and that was fixed.

Maybe someone has an idea? :)

Don't worry, fixed.