MultiPHP Manager Permission Error Linux Centos PHP-FM

Server is dedicated Linux Centos 6 Apache 2.4 Easy Apache 4 Nginx MultiPHP Manager (issue site is using 5.6) 1.On the site the PHP 5.6 is being used I am having problems with running SSH Putty commands some dont run anymore and no error is shown and no output just new line is showing again. Also not able to use the login on front end onf the website that is on the domain being used by CPanel. In Cpanel for that domain 2. I am not able to open PHP MYADMIN via CPanel but I can access it via WHM which is root user. I have used a workaround by unchecking php-fm from WHM Services Manager and then PHPMYADMIN is loading for the CPanel Account user. - But I want to know what is causing this issue I believe this is a permission issue for PHP 5.6 only, the server is not able to fully access it - for sites running PHP 7.1 there is no error and scripts are running well. I have spent 3 days looking through alot of posts and tried all sorts but unable to fix - Which server files or WHM / Cpanel configurations settings should I be checking? for the PHP 5.6 IN particular I really need help on this asap as the site is live thanks