Sorry, I forgot one thing.
Uploading files is done before the PHP script is executed. That means that the timeout is not reached until the files are completely uploaded. However, the PHP timer is started when the files start uploading.
For this reason, it has to be changed in php.ini, or in .htaccess.
Sample .htaccess file:
php_value max_execution_time 300
This will set it to 300 seconds (5 minutes). Put the .htaccess file in the same folder as the script, and it should work.
Hope that helps
-Percy