Installing and upgrading help

Ok I'm really confused. I've looked at my phpinfo() for the root httpdocs folder on my server and it lists file_uploads as ON. When I looked at the phpinfo() in the moodle root folder, file_uploads is OFF. This made me think that there must be something wrong with my .htaccess file.

--- httpdocs/moodle/.htaccess ---
php_flag magic_quotes_gpc 1
php_flag magic_quotes_runtime 0
php_flag file_uploads 1
php_flag short_open_tag 1
php_flag session.auto_start 0
php_flag session.bug_compat_warn 0
---------------------------------

is there anything else that could be affecting that configuration?

here are my phpinfo files:
http://207.44.207.137/moodle/info.php
http://207.44.207.137/info.php

any help would be greatly appreciated.