if 6v batteries arent listed, you shouldnt expect it to work.
maybe the charger is 'sensing' the battery wrong.
could be a bad charger, or it could simply be not ment to work with eachother.
although, maybe the battery is bad and that is why the charger stops charging early.
since the charger might be wrong.. it might be bad.
and with that said, you should try a different brand charger.
that isnt fair because the charger doesnt list 6v batteries as one of the supported battery types.