to troubleshoot, send yourself a test email, and see what the html links are. They should go back to your phpList installation, and then be forwarded to the final destination link. This process increments the counter in phpList.
One of two things are happening, either the links don’t go back to the server, or the counter isn’t working for some reason. If it’s the latter, you might check your version of php that is installed (use the ‘common’ plugin to view it via the phpList menus. You need a minimum of v5.4, I would recommend v5.6 or v7.x for php.