gitlib_url always set to "http://localhost:8080"

Installed using omnibus-gitlab. Changed unicorn port to 8081 and gitlab to port 8888 in /etc/gitlab/gitlab.rb

But in gitlab-shell/config.yml, gitlib_url is always set to "http://localhost:8080", which causes git operations to fail. Manually change the url to "http://localhost:8888" seems to work. But every time gitlab-ctl reconfigure cause the config.yml file to be regenerated with the wrong url.