I had some machines on an XenDesktop 5.6 farm that were not registering. [Reviewing this again, I realize that it was actually ALL of the machines] The first place I went to check was on in the Desktop’s registry to make sure the DDCs were correct: HKLM\Software\Citrix with HKLM\Software\Wow6432Node\Citrix\VirtualDesktopAgent\ListOfDDCs
WOW6432Node since this particular system was a 64 bit Windows 7 box. The registry key had both of the DDCs listed with a space between then. Check. Event Viewer just showed a generic message stating a failure to register with any DDCs.
Looking at my Eventlog on the actual DDC, I came across this message :
The Citrix Broker Service failed to determine the base settings needed for the Virtual Desktop Agent of machine ‘<FDQN>’
The stated resolution is to check generic KB article CTX126990 but the real answer for me was in CTX129644!
I had some weird licensing issue where my license server information was corrupted/blanked out. After following the instructions in CTX129644, all machines began registering fine.