What APV are you using these
batteries with? If you are using a vv or vv/vw APV, IMR batteries are recommended, or the Panasonic hybrids (which are called IMRs too). Not ICR. ECF guide on rechargeable batteries here:
http://www.e-cigarette-forum.com/forum/ecf-library/129569-rechargeable-batteries.html
As for the charger - batteries are usually charged to 4.2 volts by chargers or close to it. You can take it off the charger before that, but the charger will keep charging the battery to 4.2 volts (or close, like 4.18 volts). That's normal.
There doesn't appear to be anything wrong with your batteries or charger. The charger light will turn green when the battery is taken out, and will turn red if the battery is below 4.2 volts. You could buy an Xstar or Pila charger if you want better quality tho. These have setting that allow faster charging also. Some chargers, such as Trustfire TR-001 can take 8 hours or so to charge an 18650. An Xstar Wp II can do it in 3-4 hours in my experience.
Do you have a multi-meter? That way you can periodically check the voltage of your batts both before and after charging. Since you don't specify the voltage of both batteries before you started charging, its not possible to say if both batteries were at the same voltage to start with.