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You're nearly there!

After copying the ML files to the new memory cards, turn on the camera (with the new card inserted). It's ok if you don't see ML running at this stage. Open the Canon menu and follow the standard firmware upgrade procedure by clicking on firmware version. All this does is that it sets the boot flag on the memory card, which is required to boot ML. Simply restart the camera to make sure that it's working fine.

I did this yesterday while trying to figure out how to work off of two cards but I've noticed it's not as straight forward as you describe it (the procedure is straight forward but the results are not). There are times when the camera won't turn on even though the boot flag is on both cards. Sometimes it works and some times it doesn't.....for me at least. I've had to pull the battery several times to get it booted up again. Time will tell. Need to test it more.

When in movie mode click the info button (next to menu) a couple times and you'll see the ML settings display on the screen. Then hit the trash can to enter ML settings and all will be good. It stumped me at first too. Hope this helps.

Never mind I figured it out. There's a couple focus peaking options I've come to find. Switching to d1xy fixed it...or was it d2xy...? Never the less switching from one to the other worked. My next challenge is to master how to use magic lantern on two SD cards without having to take the battery out when I switch cards.

Hello ML community. New to the game and just starting out. Having said that, I am loving ML on my t3i overall. MY question is:

Why, when in movie/live view mode, and focus peaking enabled, am I getting small red dots ALL OVER the screen and not entirely on the objects I am focusing on? When I mess around with the focus ring they go away sometimes and focus on the object but for the most part they're always there, flickering all over the viewer. Didn't have this issue with the previous ML build. I've switched lens so maybe that has something to do with it? Perhaps f-stop, shutter, iso make a diff? Not sure. Thanks in advance folks.

My setup:
t3i
updated firmware/ML 2.3
Nifty-fifty 1.8