To set ISO when I shoot video on my 60D I just use the button on the top by the screen and use the dial to change it.
I'm assuming on the T3i you'd have to access it in the "Q" menu.
I tried that on my 60D and unless I'm in Photo Mode, it does not work. Do you set it in film mode and than go to video mode and it uses whatever you manually set it at?
Just grabbed my camera so I can check it out, here's what I did:
Turned it on, it was on "M"
Turned the dial to the video mode
Pushed the top panel ISO button
Gave me the options of 100 200 400 800 1600 3200 6400 and auto
I could select them with the dials
I couldn't change it from the "Q" menu.