Confluence Server - Linux Installer (64 bit) ignores port configuration

Debian GNU/Linux 7.7 (wheezy)
Launched the installer with sudo

Configure which ports Confluence will use.
Confluence requires two TCP ports that are not being used by any other
applications on this machine. The HTTP port is where you will access
Confluence through your browser. The Control port is used to Startup and
Shutdown Confluence.
Use default ports (HTTP: 8090, Control: 8000) - Recommended [1, Enter], Set custom value for HTTP and Control ports [2]
2
HTTP Port Number
[8090]
51000
Control Port Number
[8000]
51001

I changed the port in custom installation but the change was not reflected in server.xml. Confluence was run on default ports despite at the end of the installation it says

Your installation of Confluence 5.6.5 is now ready and can be accessed via
your browser.
Confluence 5.6.5 can be accessed at http://localhost:51000
Finishing installation ...