Quote from TheGoonior:
Are you referring to the popup that TWS displays or something Ensign is doing? TWS will prompt you if you want to accept a connection from an external API source unless you configure it otherwise. Basically, you just go to the API menu item and add the IP address 127.0.0.0 to your secure IP list.
I'm also assuming you are starting up TWS fresh every day and doing the hand login once, because unless you've had TWS disable the key-card security thing, you'll still need to do that when you first connect to your account (as far as I know).