Typically these are because of your PHP setup which is configured to run as a cgi, as opposed to an apache module, which is inherently a far more secure way to run php. However, you will find some functionalities like php_value and php_flag that will not work on less secure servers that run php as a module.
This is easily correctable though, all you need to do is put a simple container around your php_value and php_flag directives that you see on your problematic .htaccess file.
Edit your .htaccess file in your cPanel file manager or however you normally edit your .htaccess file.
Follow the example format below for your php_flag and php_value directives.
Code:
<IfModule mod_php4.c>
php_value post_max_size 20971520
php_value upload_max_filesize 20971520
php_value magic_quotes_gpc off
</IfModule>