You should be using php-cgi.exe. You could also follow the directions on how to run it as an ISAPI module.
The same thing happens on my computer running Windows XP and trying to use php.exe. I'm not even sure this is an error though. The documentation hasn't really been updated for PHP5 as far as I know. The same problem existed for me in all the release candidates and betas. I didn't know they allowed you to put the php.ini file in the PHP folder now instead of windows. That's very nice to know. It's about time.
I just found this out recently... in addition to being able to have php.ini in several different places, you can also set an environment variable (PHPRC) to tell php where to find php.ini. Thanks for that tip Walter!
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