The chip's LED is still green because SOME of the points to the chip are still connected, but not ALL of the points. The LED is always green when it's on the "ON" mode (even if it's not aligned properly), you need to switch it to "TEST" mode and then it will indicate if it's lined up right. Then align correctly again, and switch it back to "ON" mode.
Also, sometimes the chip isn't de-algned at all but it still gives the flashing red/green problem--what you do in this case is just gently press down on the chip itself--this should solve the problem. This usually only happens if the chip was installed sloppily, or if the points were a little dirty.