Security Check for WP doesn't change permissions

I have one domain on my server that will not change the permissions for files and directories. So it always shows a Red ! circle. I have it checked and save and still see the !. Other domains on the server show the green check once I check the Permissions box and hit secure. I have the WP files in a directory and have lots of other directories and files at the same level as it is our website that we are converting over the Wordpress.

I would love to get rid of the ! icon. I have...

Security Check for WP doesn't change permissions