(I am relatively new to JSS, we haven't even completed our Jump Start yet!) I was upgrading from recently installed JSS 9.96 to 9.97 on Linux and after the upgrade I could not connect over https despite having the "Finished JSS Initialization" in the logs. My own troubleshooting revealed I could open a TCP connection to 8443 but I didn't get a certificate back. Peeking at the server.xml showed me the certificate keystore was to be at /usr/local/jss/tomcat/jss.p12 – that file didn't exist. Once I restored it from /usr/local/jss/backups/.... and restarted tomcat, I was able to connect to the JSS again.
Hope this helps someone else and this bug can get corrected.
