This issue is happening this today. Never had this before. It can be in the 30 first seconds with not even 10 units yet of a game or after 40 min with 600 units. I simply lose the mouse control. I can click on the commander bar in the high left, i can click on the esc menu but i can't do anything else. No orders, no click on units or factories. The only way to solve it is to close the game and start another. This is really annoying.
Yes this seems to be happening to me as as well, about 20 mins into the game I cannot select any units or give them orders. Do not even have hundreds of units at that time.
Seems like Nvidia driver 340.52 caused the problem with me. Have restored Win8.1 to earlier image with Nvidia 335.23 installed & played for an hour without any issues.