I was attempting to film Jupiter the other night using a 5d mkiii and Magic Lantern. After 60 seconds the camera stopped but it still recorded the files. I had some issues opening the files due to missing End of File (EOF). I fixed the problem after a while by using a HEX editor to append a new EOF to the file.
I documented what I did on my blog. I hope it is of use to someone.
http://www.conorcunningham.net/blog/2014/4/10/magic-lantern-missing-end-of-file
All the best,
Conor