When performing an unattended install of XenDesktop the server will join the farm in indirect mode, making it dependent on the server specified in the command line e.g.

setup.exe -passive -edition ADV -joinfarm %JOINSERVER% -components DDC,CONSOLES -licenseserver %LICENSESERVER% -nosites

To convert the server to direct mode run the CHFARM utility:

chfarm /joinfarm /ddsc:"SQL Server" /odbcuser:%USERNAME% /odbcpwd:%PASSWORD% /dsnfile:MF20.dsn /verbose /quiet

Desktop Delivery Controller 2.0 Administrator's Guide
http://support.citrix.com/article/CTX116843
P87. Installing Controllers Using Setup.exe