Citrix XenApp 5 or 4.5FP2 has got a bug - when you launch CMC and run the discovery, it does not find the XenApp farm, only the Web Interface module.
To fix it, run the following:
cd %CommonProgramFiles%\Citrix\*Present*
%windir%\microsoft.net\framework\v2.0.50727\regasm /codebase pse.core.dll
cd %CommonProgramFiles%\Citrix\*Framew*
CmiLaunch.exe
Run the discovery again and it should find it now
