I dunno if anyone has experienced this and has a solution because at the moment I might just try the 'ol reinstall windows route:

The problem is sometimes in Windows my mouse clicks dont register, and i have to click again. This is a general windows thing, doesnt matter what app. Ive not been aware of it in games, but thats not to say it does or doesnt happen. Though you would have thought playing a shooter like CoD you would notice if the gun didnt fire!

Any ideas? and yes I have virus protection, use adware and have a firewall...

Doesnt make any sense to me :/ I might end up reinstalling windows, as unless someone has experienced it its unlikely anyone will have a solution to this weird problem.