To fix this problem plug in your controller (the red light should come on for a few seconds) when the green light comes on unplug the controller and plug it in again, continue this process until the red light stays on. This can take any where from 10-30 times till it works, the reasoning behind this?
Ni-Mh battery's loose 30% charge in this first day with no use, then the charge rate decreases and will completely discharge at room temperature in about 30 days. The problem that you have ran into is that the battery is so slow that it wont except a charge. The capacitance of the battery its self is changing polarity to a near neutral when it reaches such a dead point. By forcing the recharge on the battery over and over again you are giving the battery enough of a charge to allow it to recharge as per normal again.
I hope this helps you and any one else who comes across this problem!LightSpecter101

This should work. Same thing happens with all rechargable batteries. Technology hasn'y yet discovered how to prevent a rechargable bettery from having a 'memory.' What I mean is batteries that you can recharge ie. cellphone, 360/ps3/wii controller have a 'memory.' If you charge the battery full way and use it until it's about fifty percent, then put it on the charger again, the battery will remember that fifty percent is where it sould get charged so it will think that fifty percent is where it should 'die.' That is why most people at the cell phone stores tell you to only charge the battery when its almost dead.