I don't think this is because of the Magic lantern but I wanted to post it in case someone else saw a similar problem. My T3i has stopped auto focusing in P, Tv, Av, M and A-Dep but still auto focuses in all the auto modes and Video modes. The camera is 3 months old and I have sent it back the first time after only having it for a month to have it fixed. They fixed it (didn't tell me what they fix) but a month later it started doing it again. I shoot a lot of time lapse with ML and use the video tools quite a bit and other than the AF issue everything else seams to work fine.
Thanks to the ML team you guys rock.