I played in a friendly brawl against my partner - him playing Elenda, Saint of Dusk (lifegain) and I playing Lord Xander, the Collector (opponent mill). I started with the usual 99 cards in the library minues the initial hand, and he started with 40 cards in his library. Since I was playing mill, I won the game very quickly since he had the equivalent of starting a game with less than half his "life total". We checked in case it was only a display issue, but no, only 40 cards and, after being milled, only 40 cards in the graveyard and he lost the game. We've played this exact combination of commanders against each other before with no issues, both decks containing 99 cards as usual. This seemed to be a one time thing.