By any chance, is the file readonly?
The Beautify command is enabled for me in a writable PHP file, but it wants to run the HTML beautifier.
It sounds like in the past you had told SE that php should behave like c (i.e. php refers to c).
In 2008 you can do the same thing:
Go to Tools->Options,
Click the Language node,
Click the Application Languages node,
Click the C/C++ node,
Click the General node,
Click the Edit These Extensions button,
Click the + button,
Type "php" in the box,
Click OK on the dialogs to dismiss them.
It won't take effect on files that are already open, though. You will need to close/reopen them.