I believe Charlotte lost the memory of her mother's maiden name because someone has gone back in time and changed something. It is sort of the opposite of what happened to Des when Dan met him at the hatch. Dan changed something in Desmond's past, and then in the actual real world present Desmond all of a sudden 'remembered' it.
So someone went back to the past and did something that changed Charlotte's mother somehow. This of course gets more and more speculative, but if we assume that Charlotte does have some connection to the island, either being born there or something similar, than it would be completely plausible that our characters will run into Charlotte's parents or whatever. It's just like in Back to the Future when Marty's siblings start disappearing from the photo. I know that Daniel says it isn't possible to change the past, but I think he's either wrong or doesn't fully understand who is exempt from the rules. It would be pretty freaky, but maybe something happens which kills Charlotte's mother before Charlotte is even born? Charlotte didn't really explain whether she lost that memory temporarily or if she still can't remember. If it was permanent, then that gives my ideas some strength. If it was temporary, then I would add another layer and say that someone went back and changed the past, then someone went back again to fix whatever the first person did!