Different chargers just behave in different ways.
I've had chargers (both USB cigalike, and big battery AC chargers) that will go from red while charging, then immediately switch to green when fully charged. Others would be red while charging, then blink red when close to full charge, and then switch to green when full. Some were red when charging, and then no light at all when done. I've had a few that would be red when charging, orange-colored when almost fully charged, and green when fully charged.
It just depends on the choice the manufacturer makes on how to alert you to a fully charged battery.
Whatever the specific method of charge indication, the charger knows when the battery is fully charged, not by time, but by voltage. The charger will charge the battery until it reaches appropriate fully-charged voltages (usually around 4.2v, which can vary obviously)
In my experience when a charger goes bad, it goes bad, either completely stops working or won't do anything when a battery is hooked up. I'm sure your charger and
batteries are just fine.
EDIT:
After re-reading your post, it seems I was a bit confused. I thought you were comparing a volt charger to a V2 charger, but you are getting different behavior from different
batteries on the same charger. I get it now.
As far as the light on the end of the battery staying lit, that depends on the circuitry in the battery, whether or not the manufacturer wanted the light to stay constantly lit when charging, or just blink a few times and then go dark.
The changing light on the charger... that one I'm far less certain about. The only thing I can think of is some sort of filter or protection circuit in the battery that's stopping the charger or giving some sort of feedback that is confusing the charger, hopefully someone with more expertise will chime in.
