Yes, Domain Controllers should be Master Browsers - setting your domain controllers as "Preferred Master" should fix most of the Master Browser election problem.
One of the common reasons for operating a WINS server is to provide a central reference for NetBIOS names across several subnets. Choosing one primary WINS server and pointing all clients to it lets NetBIOS name resolution work across subnets without requiring the use of Domain Controllers.
But if your system is supposed to rely on domain controllers, loss of replication for site C may explain your symptoms. So start with verifying successful replication.
Setting the IsDomainMaster parameter entry to True or Yes makes that computer a Preferred Master Browser which has priority over other computers in master browser elections. Whenever a preferred master browser starts, it forces a browser election. Any computer running Windows NT Workstation or Windows NT Server can be configured as a preferred master browser. If no other condition prevents it, the preferred master browser will always win the election. Set the parameter in the following registry path:
Hive: HKEY_LOCAL_MACHINE
Key: SYSTEM\CurrentControlSet\Services\Browser\Parameters
Type: REG_SZ
Name: IsDomainMaster
Value: True
Key: SYSTEM\CurrentControlSet\Services\Browser\Parameters
Type: REG_SZ
Name: IsDomainMaster
Value: True
REFERENCES
http://www.windowsnetworking.com/kbase/windowstips/windowsnt/registrytips/network/preferredmasterbrowser.html
http://serverfault.com/questions/239066/which-machines-should-be-running-as-master-browser
