Clouds Over Brooklyn Time Lapse

I'm trying some new time lapse techniques, and shot this from my roof yesterday:

My little Nikon (P6000) has a built in time lapse mode, that takes photos and compresses them automatically. I made this time lapse by shooting lots of individual pictures with the P6000's built in intervalometer, and then used using HandyAVI and the Accusoft Picvideo Motion JPEG encoder to make them into a motion JPG movie.  I then let Vimeo compress it.  There's still a few glitches but overall I think it looks OK.  Now, if I can just get my Nikon D90 to behave--when I shoot with an intervalometer on that camera, I get some weird movement inside the frame.