Have a black stripes when recording Timelapse

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I Have a black stripes when recording Timelapse in RAW.
Settings: Canon 600d, 14 bit, 1 fps, 1 shutter speed, max resolution, 18 mm angle.
Also I used nd filter fotga, i think this a reason.
But when i record a simple video there is no stripes, its ok.
Help me, what can i do - change settings or dont use nd filter?

https://youtu.be/qW72qLyHe1c