Public download links and logout URL is built from the hostname and the domaine name of your server. So, probably, your servername is xxx and your primary domain name is xxx.domain.com. You can either fix this (set domain.com as your primary domain) or manually configure your logout URL and public links:
db configuration setprop ajaxplorer PublicDownloadUrl http://xxx.domain.com/ajxppub LogoutUrl http://xxx.domain.com
signal-event webapps-update
Regards, Daniel