Maverick,
Batman Begins/Dark Knight, as has been stated, are a completely new continuity. They have nothing to do with the earlier films.
Think of it this way:
The Daniel Craig's James Bond in Casino Royale is NOT the same James Bond that Connery, Lazenby and Moore played (these three all had continuity, including the mention in The Spy Who Loved Me and For Your Eyes Only of Bond's wife, killed by Blofeld in OHMSS).
Also, the Penguin as a deformed mutant was ENTIRELY the invention of Tim Burton. The original Penguin was actually one of the most "normal" (physically and mentally) of the major Batman villains.