I had this same problem with mine recently. Freenas for some reason will always lose the election for master browser. Not only lose but get kicked by another machine coming on the network as well if it was master browser. A google search will result in several references to a couple of registry entries to add to a windows machine to prevent a workstation from winning the election but they don't work. Even my open-elec-plex box was kicking freenas from master browser when I turned it on.
First you have to disable the computer browser service on all your windows machines. Then add these lines to the auxiliary parameters in the CIFS settings menu in the services tab in Freenas
Code:
domain master = Yes
preferred master = Yes
os level = 65
Haven't had the problem since.