Ok, I got it to work now. I think I've figured it out.
I've been using htaccess for different versions of php. I ended up deleting it and use the 'Web Features' and select the php I want to use instead.
Questions:
1. For a directory for example <domain>/dir, I used htaccess for a different php version. Will this also change with the setting made in Advanced PHP Configure > Disable Functions as well? Or how do I made the changes?
2. Do we have to actually select the actual php used in 'Web Features' each and every time we all a new client or domain?
3. I use a WordPress plugin on all my WordPress that recommends these off too.
PHP Display Startup Errors
PHP Expose PHP
PHP MySQL Allow Persistent Connections
But there no options for that in 'Advanced PHP Configure'. How can I make the changes so on next update it will not go back to default again?