It does still flag the folder and a registry entry for the start menu. I do know that on the 2005-11-25 release it flagged one more directory (Which was the Start Menu folder) than with the 2005-12-2 release.

But it is still flagging the Phoenix folder in Program Files and the registry entry HKEY_USERS\S-1-5-21-183062753-716789552-782984527-1054\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu\Programs\Phoenix.