I was getting that same issue with the blinking red lights whenever I charged my controllers. The reason why you get a red flashing signal is that you have a bad connection while charging. What you have to do is remove the battery pack from the controller and with a small flat screw driver bend back the positive metal prong on the battery pack (careful not to bend back too far). That should give it a good contact and will eliminate the flashing red light.
8 months ago