I have the exact same issue on my computer (which is not a laptop).
It happens even in Safe Mode, and even with my video drivers completely removed -- and also when completely reinstalled.
The login screen is not affected, nor is the Ctrl+Alt+Suppr screen -- Only the desktop is.
When I let the blinking going on and on, at some point after several minutes, even hours, it stops and the computer is usable as before.
I don't understand, and I am about to revert to Windows 8.1 to be able to use my computer normally :/
[Edit] It seems to be linked to Cortana / Start Menu -- Killing "Shell Infrastructure Host" will stop the blinking, but a critical error will popup, warning that Cortana / Start Menu cannot be loaded. -- The computer is still not usable then, and any Metro
app / setting is inaccessible neither.