Blinking lights on the "Rock Band" guitar controller indicates it is having an issue connecting the console. This problem can be fixed by re-syncing the controller and guitar together. The steps for doing this are almost identical for the PlayStation 3, Wii and Xbox 360 versions. The only difference is the location of the "Sync" button for the console. The blinking lights can also be a warning of low batteries, which can be fixed by replacing the batteries.
Plug the "Rock Band" wireless dongle into the USB port on the console. This step needs to be performed on the PlayStation 3 and Wii versions only. The Xbox 360 version does not use a wireless dongle.
Turn the console and guitar controller on.
Press the console "Sync" button. This is the small, circle button located next to the disc drive on the Xbox 360. The "Sync" button for the PlayStation 3 and Wii versions is the small button on the wireless dongle.
Press the guitar "Sync" button on the "Rock Band" controller. This is the small white button located near the whammy bar on the front of the guitar. The lights on the guitar stop flashing after a few seconds to indicate the guitar and console are properly synced.
Switch the power switch to the "Off" position.
Remove the battery compartment hatch. It is located on the back of the guitar controller next to the power switch. The PlayStation 3 version has a screw that needs to be removed first.
Replace the batteries with three new AA batteries. Replace the battery compartment hatch onto the guitar.
Switch the power switch to the "On" position. Press the button with the lights to turn the guitar on. If the issue was low battery life, the lights should no longer blink.
The "Rock Band" and "Guitar Hero" guitar controllers on the PlayStation 3 and Wii versions use similar wireless dongles. These are not interchangeable. The "Rock Band" guitar can connect to the console through the "Rock Band" wireless dongle only. It is possible for players to be unable to connect to the console because they accidentally swapped the two wireless dongles. This is not an issue for the Xbox 360 version, because the guitar is able to connect directly to the console.