I'll be interested to hear what happens. Using one slot can also isolate if it is one bad battery or if it's the charger. That charger only has one LED so if any battery in the pair is charging still, then it stays red and has no way to display that one battery is charged and the other is not. If you have a bad battery, then it might not charge properly and the charger continues to display the red light....
I've had that happen.
Also, sometimes charging faster (or even slower in some cases) can get a battery working right again if it is having a problem. Electrolyte formulas are finicky sometimes, so giving them a nudge by fast charging or letting them charge forever on a very slow charger can sometimes get the electrolyte reacting the way it is supposed to. So, if one of your batteries turns out to be bad, then there is also a chance to get it working right by fast charging it at the full 650 mah once or twice.