Travis,
The only reason your other sites run PHP (what applications, sites do you have running PHP?) is because you must be lucky.
If you can't get a normal PHP page to return back the proper information then I don't see how other sites work.
Following the directions on the site I supplied has allowed every 2003 Server I've setup (about 7 or 8 of them) to run PHP properly.
PHP is PHP and not dependent on running UBBT or some other Web application. Each application may have other requirements for add-ons or security settings but plain old PHP should be able to run all the basic commands.
My guess is that you kept a copy of php.ini in the C:\WINDOWS folder even though you're not supposed to. Somewhere, somehow the system is probably seeing conflicting information.
You also need to have security setup for certain folders such as the %temp% folder in Windows.
