The problem is that the agent machines which are displaying the FQDN names have "agentname" field defined in the Configuration. The value of this field is the FQDN name of the agent, which is displayed in explorer. If we find this field defined in configuration, we use the value of this field to be displayed. In the agent machines with short names, the field is not defined.
In order to deal with the problem and only have Netbios names listed within DSM Explorer, on the FQDN agents, run:
ccnfcmda -cmd setparametervalue -ps itrm/agent -pn agentname -v ""
(agentname is not listed in the configuration policy in DSM Explorer so it can only be changed by above command)
Also make sure the OS name is being used by running following command:
ccnfcmda -cmd setparametervalue -ps itrm/agent -pn useosname -v 1
Alternatively, it can be set in the GUI:
Finally, wait for the agent to reregister itself (by default once a day) or force reregistration immediately using the command "caf register all"