I am not familiar with PB-E2 or Canon system. So I could be wrong. But I am trying to help. So please do not shoot me .
IMHO, if the battery (Ni-MH) with different capacity put together in series, the lower capacity Ni-MH battery can dry/finish first. Afterthat, the 'still have power' battery can charging the dry/finish battery (but with wrong polarity). It is not good, since charging the battery with wrong polarity could caused the battery to leaking.