Unless you think of the writers of Heroes as a bunch of 12 year old boys, the plots aren't going to make a whole lot of sense. They put stuff in because they think it's cool and works for the time being, without actually considering continuity or precedence.

It's fun to try to figure this stuff out but it is a fruitless effort. Any explanation the writers or producers give to these inconsistencies are nothing more than copouts come up with at the last minute to throw fans a small bone. Plenty of shows have rewritten the history or contradicted established context occassionally, but Heroes takes the cake by managing to do this so frequently. It's ridiculous.

Entertaining show, though.