I've been using Magic Lantern for a week and while it's great, I have one problem with it. If I try to use an wireless flash, it works... for a while. But after a few hours, it stops synchronizing -- eg: the external flash is firing, but it isn't in sync with the curtains so all my pictures are underexposed. If I increase the time, about 1/60 or higher, a part of the picture is exposed correctly (the upper part). It seems that the external flash fires before the picture is taken. This doesn't happen with the original firmware and it appeared after I've installed Magic Lantern, although it worked fine in the begining.
Reinstalling original firmware and clearing the settings clear the issue.