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Thanks for the reply.
The problem was the bug since I used the settings that you mentioned.

About the video, it was MLV. I tried recording again it was working without a problem. I think the file somehow corrupted.

I tried to shoot time lapse in 3x crop mode. But the files are posterized. I don't know if the dng files are corrupted or another issue.
Settings: Basic silent picture in Video crop mode. FPS override. Shooting interval : 30 Seconds. Magiclantern-Nightly.2016Jan15.EOSM202
Sample DNG file :https://drive.google.com/file/d/0B5vPhFcWMEVic1l4SmJ1ZW9VWEk/view?pref=2&pli=1

Also sometimes intervalometer stops after the first picture in Full Silent Picture mode. The only fix that I know is to remove the battery and try again

Responding to the FPS override changes:

At  45.02 fps in 3x crop, horizontal pink lines are visible. I think this is because of changing shutter speed. it showed 0" when I was testing different shutters.
Also at 720p in no crop mode, maximum fps is 31.23.