I had that come up a couple times too. It's fixed in the current Git versions because I just made it so that the convex hull algorithm is always run when creating poly shapes. I'm getting pretty close to releasing 6.1, so it should be pretty stable.
The issue in 6.0.3 is that slightly different measures are used in the convex hull algorithm and the validate function so there are floating point precision issues. The Git code also has a function that allows you to create convex hulls with a distance tolerance. Points on the hull that contribute to the shape by less than the tolerance are dropped, creating simpler polygons.
Thanks, I'll check out the github version - although last time I tried to checkout chipmunk pro from git it wasn't able to pull, probably need to be using a different github client.