At the moment on the PVE NA servers. We're having the same problem - it seems like the old flags are under the old rules system and we're currently losing land.
If the owner who planted the flag doesn't walk on the claimed land it can be taken. Not the COMPANY MEMBERS but the person who planted the flag? WTH kind of logic is that if you leave a company all items you own stay with the company why in all things holy would that mean flags should work differently?