While the DevTeam rightly asserts that Apple can't undo the bug exploited by PwnageTool via firmware update alone, it's still subject to the whims of iTunes connectivity. In fact, iTunes 8 seems to detect jailbroken devices jailbreaking attempts and then stomps its feet and refuses to play nice. While the DevTeam says that fixes are in the works, the growing list of useful applications in the AppStore coupled with the global retail availability of the iPhone (and lack of a 3G unlock) makes PwnageTool less and less relevant with each passing day.
Update: The problem seems to occur when you try to restore to an iPwned ipsw from a non-iPwned device. Syncing to an already Pwned device works fine.