Receiving the warning above? in a Citrix XenDesktop 5.6 (FP1) environment running on VMWare vSphere? The problem lies in the order of installing VMWare Tools and the Citrix Virtual Desktop Agent.
First, install VMWare Tools, then install the Citrix Virtual Desktop Agent.
Also, in some environments, http://support.citrix.com/article/CTX130851 could be usefull.