502 error with nginx after stop services in CentOS

I am currently running server version 5.1.3 on CentOS 7.
I installed it using the automated script on github.
Basically I want to upgrade to the latest version of Seafile server.
Whenever I run the commands

./seafile.sh stop
./seahub.sh stop

the services stop as expected.
When I try and start them again, they seem to start fine with no errors.
But when I try and access the web portal, I get a 502 bad gateway error. Even after a reboot I still can’t access the web portal. Only way I was able to recover was using a snapshot I created before making changes (virtual server).
Anyone have any suggestions as to why this is happening?

Please check if the seafile and seahub processes are still running. Also see what you can find in the *.log file in logs/ directory.

I ran top and checked the commands that were running for the processes and compared that to the processes when the server is freshly booted.
This is the command (not complete) that is run at boot (that works properly):

python2.7 /opt/seafile/seafile-server-5.1.3/seahub/manage.py runfcgi host=127.0.0.1 port=8000 pidfile=/opt/seafile/seafile-server-5.1.3/runtime/seahub.pid outlog=/opt/seafi …

This is the command that the ./____ start runs instead (and doesn’t work):

python2.7 /opt/seafile/seafile-server-5.1.3/seahub/thirdpart/gunicorn seahub.wsgi:application -c /opt/seafile/seafile-server-5.1.3/runtime/seahub.conf -b 0.0.0.0:8000 --pre …

Either the seafile.sh or the seahub.sh file run something almost completely different to whatever the boot command is.
To prove my theory, I manually stopped the services and then simply rebooted. The services started back up fine.
If I manually stop THEN manually start them again, then I can never get the services to start properly again.

Surely I’m not the only one who’s created a server using the automated script and come across the same issue?