Ken says he has three batteries but only two phones. That means that at least one battery must have been stored out of a unit. A battery stored inside a unit, even seemingly switched off, would eventually drain and possibly die but a battery stored outside should not, unless it was stored depleted to start with.

Perhaps a thorough investigation is called for? Put one N900 aside and ignore it for the time being. Try all three batteries in the other unit. Then swao the units and try all three batteries again.