Yeah, its like there are three modes - during recording, during scrubbing (while editing, but is probably the same as live recordings as well), and during a media export. During scrubbing it approximates the final rendering to keep it real-time, but the final export takes as long as it needs to get it perfect. So you do get these differences. Sometimes I put a dragger on the elbow of the arm for example to sneak in a few frames here and there to make sure the elbow hinges in the right direction. So it is known that during the different modes you don’t get identical behavior.
But how different are you talking about? Maybe something else is going on as well...