So if I read you correctly, the PE stepsize wasn't tied into the Graphics stepsize hence the problem.
Thus, the Physics Simulation was taking steps at 70Hz irregardless of the simulation clock (render clock), allowing multiple PE steps for every one Graphics step or vice versa, too few Physics steps for every one graphics step (if fps_max=140 for example). Something like this?
If this is the case, is this bug related to our stepsize discussion from before?
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I will change this behavior so that user forces are applied throughout the entire time of a "wait()" statement.
I would be interested in hearing more details of the solution once the above problem is more fully understood by us "out here". 
If the above is the problem, I would suggest a scheme that explicitly ties in the Physics and Graphics clock in discrete intervals. For example, so you can set the PE clock to run twice as fast as teh Graphics clock when accuracy is desired or half as fast if your simulation values performance over accuracy.
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Please note that this is likely to break existing code if you explicitely set forces/torques in your script.
Marco, I'm guessing that would be EVERYONE using the PE? 
Here's looking forward to THAT!
