I could not solve it by using Quicktime. Realtime compression and 64 render samples gave me half-smooth half choppy render, but it's not enough. There may be a bug in the encoder.
However, it worked fine with PNG, RGBA, %0 compression. And, you have more control over your video when you render it as an image sequence.
You can import PNG sequence to Blender and export it again as a video file format, or you can use other video editing softwares to give its final shape.
Does that solve your problem?