Help with subdomains
If sld.tld/subdomainroot/Y works, that suggests that you have set $base_url in your settings.php to include subdomainroot.  If that's the case, subdomain.sld.tld/Y certainly won't work because drupal will be using the above.  Now, if this is the case, and you change the above to subdomain.sld.tld, you still may have issues with cookies being set to the old domain until they are cleared.