Thanks for the heads up R0jo, I guess that happens to all of us sometimes. I could do an "ugly" solution just by pinning impressions over the sprites but then I would need to have a pinned sprite on top of each body part of the ragdoll to later show damaged body parts for example (so it's not really that good option...) Being also a bit of a perfectionist in optimizing things to the extreme, I wouldn't be satisfied by makeshift solution that would clutter things unnecessarily...
so I'll continue looking into the source, and if I make any progress pinpointing a possible solution I'll post here... luckily the commenting is very good (I'm really impressed with your work... I even was able to get rather good performance on the first iPad when using Chipmunk physics).
Just like R0j0 said, it's best to recreate control logic with chipmunk..if you're mixing several behaviors together, you sooner or later will face situation where the logics are clashing... if you're making a car game, you could make acceleration by tweening a value towards certain velocity, for example) - I would recommend at least completely rethinking what things you need for the game, and defining them.. then think how to do them with chipmunk (it's very diverse).