I've never done a comparative test, but by instinct, during a long exposure I always flash the model in the middle of the exposure, rather than at the end. My idea is that by the middle of the exposure the model should be relaxed, but still. I'd imagine that any movement is likely to be at the beginning of a pose (when they settle-in) or at the end (when they are cold/bored/fed-up).
Hope this helps