You know, that actually really confused me, as well... I was also confused when, in episode 62, Chibiusa thought that maybe Ami had the Silver Crystal; but, didn't she already establish that she knew it was Usagi who held it? So confusing...
Anyway, I've always heard the theory that Chibiusa doesn't recognize Usagi as her mother because present!Usagi acts nothing like Neo Queen Serenity... I'm sure that's true, but it still doesn't explain everything... Hmm... I'd like to know, too!