Instructions
Hold down the "Guide" button on the wireless controller for three seconds, then turn the controller off. If you have multiple controllers connected to the Xbox 360, you will need to disconnect all of them in order to resolve the issue with the one controller that's blinking.
Turn on the Xbox 360. Press and hold down the "Guide" button on the controller that had the blinking lights.
Press the "Connect" button on the front of the Xbox 360. This button is underneath the "Power" button on the console.
Press the "Connect" button on the back of the controller. This must be done within 20 seconds of pressing the "Connect" button on the Xbox 360. If too much time elapses, just repeat previous step.
Wait a few seconds until the lights around the power button on the console stop flashing. When they stop flashing, the two devices are now connected.