Homer I have this problem too, when my controller vibrates sometimes...
It's because I dropped the controller too many times and the battery pack loosens when ever it vibrates, causing the controller to shut off....as if I'm taking off the battery pack to put new ones in. Maybe it was because of dropping it sometimes? That's my only guess.
No its not normal for the light to be blinking. My wireless does this after 6 months old or so. I figured the problem has something to do with the battery pack connection wearing off or something due to repeated taking out and replacing of the battery capsule. I switched to a wired controller and all these problems disappeared.
Driving a PC racer with the keyboard is about as effective as typing an e-mail with your car's steering wheel. ~ Brian Ekberg
I've heard of this issue before with various games. The only solution I can think of, is that perhaps at the point it's telling you to reconnect your controller, the game tells your controller to vibrate, but the vibrate mechanism is somehow messed up. So try turning vibrations off if they're on, and see if that helps. If it does, it's your controller.