Hi. Lets see if I am following you correctly... you did a great job of describing the potential problem. I don't have a VC2 that I can find but a VC4. I often have one battery connecter slot do something similar. Is the battery warm to touch ? 97% or a bit over 4.15 volts on the charger screen is about as much as I would charge them. You could go for the full 4.2 v. If the saber is working properly then I would just go with it. Use the saber on a regular basis and let the battery power go down to about 20% and even completely drained before placing back into the charger... for at least the first time. Don't leave them totally drained or they may eventually lose the recharge memory... but this charger has the ability to sort of wake the battery up if able.
A spare set of Li-Ions is a must and I have many spare batteries that are charged and stored in a plastic container. They keep their charge for many months but I do check them every 2 months or so. Have gotten a bit lazy on that.
There are many different theories about when to charge and how to store batteries. Personally I have had good results not keeping them on the trickle charge and I'm sure that there are many more members that do the same. The batteries that are in the saber are not sent at full charge. The extra ones that come in their individual boxes are at about 45 - 60% and are good to be left that way. Still should be checked now and then and stored safely.
If in doubt contact US as sometimes a malfunctioning battery has been sent with a saber.