I found it to be working as expected. Do you face this issue on a specific scenario?
Also are you on Win or Mac?
I am on Windows 7
Did you clear Preferences (Ctrl + U) in Flash CC . ("Reset all Warning dialogues")
Then executing a jsfl script from command line with "-AlwaysRunJSFL" option, opens a dialogue asking whether to Run or Open the script.
Flash CC should respect "-AlwaysRunJSFL" option and Run the script.