Run php --ini
to find out which config files are loaded.
CLI could use another config-file than php.ini.
EDIT:
Make sure the file got these things correct:
extension_dir
This should point to your extension-directory. There may be a line there which you could just uncomment. Otherwise it's probably "ext/" or something like that.
Also, make sure
extension=php_mcrypt.dll
is uncommented.
You can use php -info
to check what extensions are available.