Are you using the CodeIgniter framework that came with the Cpanel Installatron
I was building a website using code igniter framework as well. I had .htaccess as below.. After login, I'm being kicked out to login screen again.. do you find anything wrong with below .htaccess file under public_html folder?
RewriteEngine on
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L,QSA]