Bumping a very old thread, but I see there was a 02/15 post on page 4.
I have a MSI Z77A-G45, with win 8.1 pro fully updated, but other than that, not many programs installed (says 37 in programs and features, but a lot of those are Nvidia and C++ etc.) Anyway...
My issue was getting to the desktop after start up from "shut down" ,but then the loading wheel animation would freeze, and the desktop would become unresponsive with anything I clicked on failing to respond or being opaque.
After trying refresh your PC (which meant I had to re-install everything - as you will all likely know) it still happened.
So I did what I should have done at first, which was disable any special BIOS features for boot, all of the start up items (i.e taskmanager>startup), and any scheduled tasks I had set to run on log on.
Then by process of adding one back at a time and rebooting, for me it turned out it was core temp. http://www.alcpu.com/CoreTemp/ I love this little program, but for now, it's gotta go. I have rebooted about 10 times without it, all fine, and about 5 times
with it set to run and not set to run but launching it and each time I get the same freeze.
Could be some other conflict with a program/app you are running different to my issue, but I think the general idea of disabling as much as you can from running at start up, and then working through enabling and rebooting one by one should help isolate.
This may be a little different to the awake from sleep state issue mentioend in this thread, but I have 64bit windows which that issue apparently doesn't apply to.
Anyway, there's my 5 cents for the Community.
Good luck troublshooting all.