anhalt
Hello,
I’ve not seen this particular issue before, but I suspect what may be happening is that the Specify process is running as the webserver user which typically has $HOME set to /var/www/. The Specify 6 code that is used by the workbench tries to write some logs and preferences in the $HOME/Specify subdirectory. I would check the apache.conf that sets up the Specify 7 instance. There should be a line similar to this line (https://github.com/specify/specify7/blob/master/specifyweb_apache.conf#L19) in the example conf file. Make sure the user specified there is a regular, non root or daemon user.
Ben