Anyone familiar with Cisco equipment will know that after you enter a command and hit carriage return the affects will be immediate on the running state.
Cisco(config)# interface gigabitethernet0/1 Cisco(config-if)# shutdown
With Fortigate one gotcha that catches a lot of people is the use of the end command. Until you type end and hit enter your commands will not affect the state of your device.
FG # conf system interface FG (interface) # edit wan1 FG (wan1) # set status down FG (wan1) # end