Content links are breaking
Your woes are most likely coming from apache (or whichever web server you are using) unless you are using the domain module. Either your .htacces file or virtual host (depending on whether you have "AllowOverride" on in apache) should be setup to route requests through 'example.com' and not 'server.example.com'. 

Are you on a VPS or shared host? What flavor of Linux are you using?