Not sure what is the problem with your computer, but perhaps you were just reading it wrong. The capacity % is not for the charge, it is how much charge the battery is able to fully charge as opposed to when it was brand new. So 100% Capacity battery with a 100% charge means the battery is at its best. But a 12% capacity at 100% charge means your battery will only give you 12% discharge time.... 50% charge is only 6% of the overall charge.

My laptop battery is now at 72% with currently a 99% charge.

Hope that helps.
-aj