Chances are, if you're looking for a fix to this problem, you are running on a server that once ran PHP4 or older versions of PHP5. Since PHP 5.3, the php.ini file structure has changed and using an older PHP.ini file can cause problems with PHP5.4. Simply rename the php.ini file in your root user directory and it should clear up the problem. Look at the phpinfo page for the location to a loaded php.ini file on the system and copy it over to use if you still need to use it. Some setups (I believe suPHP) use .user.ini instead of php.ini.
One other place to check is "register_globals". Make sure it is set to Off