When upgrading an existing Confluence instance using the Windows or Linux installers, custom ports in the server.xml are not transferred to the upgraded version.

Steps to Reproduce

1. Install Confluence 5.6.0 and configure a custom port
2. Upgrade to 5.6.1 using the installer, and confirm that the port is preserved
3. Upgrade to Confluence 5.9.1 or above, confirm that the port is now back to the default of 8090 in the server.xml

Fix
Edit the server.xml and correct the port number. You can find the old port number in the server.xml in the installation directory backup created by the installer.