I seem to get a much cleaner install doing it without the help of the installer. I just copy the php_*.dll of the extensions I plan to use to \system32 put php.ini in the \winnt\ and make a few changes to it and the default site adding .php .phtml .php3 and told iis to use index.php, index.php3 as it would default.htm, etc...
BTW I'm using the php.exe
CT