We use suPHP in all of our servers. This is the common reason why php_flag or php_value doesn't work on CH servers. To change a value like "register_globals" or other you need to use a custom php.ini file put in the public_html folder. Suppose, if you want to change the value of register_globals using a custom php.ini file, just put the following inside a php.ini file created on your public_html folder:
Learn how to change a php.ini value.
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