I had the same problem with my project, but the resolution I’m using is 2880 x 810 and I had to use the highest quality image as possible since the video would be projected onto a big building, and I had over 450 layers of video. Anyway, it took ages to render less than a minute video and the avi file is HUGE! When I played the avi it was really jerky as well.
I brought the footage into Windows Media Encoder and it got rid of the problem, it played beautifully. However, it depends on what you want the final file format to be. I hope this could help you a little.
Good luck.