Alkaline batteries that are NOT rechargeable have a higher voltage than rechargeable batteries.
At their peak, fully charged state, they're close to 1.65v but they'll quickly discharge to around 1.5v and then gradually discharge and give most of the energy until you get near 1v.
Rechargeable batteries are different, their nominal voltage is 1.2v and when they're fully charged they're close to 1.35v - it's quite possible your charger simply stops charging them at 1.31v (a bit below 1.35v as safety)
Just like the regular alkaline batteries, rechargeable batteries will give most of their energy down to around 1v.