Security updates or system restart break ssl certificate.

I recently installed the VMDK release of the torrent server(v14.1) VA and I installed the security updates. However once everything was ready I noticed that I could not access anything except for the webmin panel. After looking through the logs I found that nginx failed to start with an ssl cert problem so I decided to reinstall.

After reinstalling everything was working well, till I rebooted. In both instances I get this error(from deamon.log)

Mar 14 02:59:14 torrentserver nginx[497]: nginx: [emerg] SSL_CTX_use_PrivateKey_file("/etc/ssl/private/cert.key") failed (SSL: error:0B080074:x509 certificate routines:X509_check_private_key:key values mismatch)
Mar 14 02:59:14 torrentserver nginx[497]: nginx: configuration file /etc/nginx/nginx.conf test failed
Mar 14 02:59:14 torrentserver systemd[1]: nginx.service: control process exited, code=exited status=1
Mar 14 02:59:14 torrentserver systemd[1]: Unit nginx.service entered failed state.

Is there an easy and permanent fix for this or is it something that turnkey has to sort out?

Thanks!