I found out something yesterday that may be part of the cause.
I use php includes and have to paste a line of code in myhtaccess file. That information recently changed, I had skipped a couple sites in updating and so anything in the php includes was not showing.
Lol, if they can't see it, they sure can't click on it! You might want to check your sites that they are up and your php includes are showing.
That update was
AddHandler application/x-httpd-php5 .php .php4 .php3 .phtml php php3 php4 php5 php6 .html