Thank you all guys.

Yes Gordon, clouds were moving pretty fast, on a time lapse above made with my old Canon 1000D I went for max ISO 1600, to cut exposure time, that's why is noisy.
On time lapse below made with Canon 7D I have used ISO 3200 and have been able to cut exposure to 8 seconds and I have used extreme wide angle lens which also helped with clouds movement.

Here is a new time lapse from that night, and is much better quality the previous one http://youtu.be/j_xmypY6lgo