On the first run of some scripts, the plots and message window are updated during the course of the run. However, on rerun, it looks more like the messages and plots are all written/updated suddenly at the end of the run. Also, solver windows appear in a different location on rerun.
Also, the OpenGL plot (at least) is incomplete on the first run - stars, text, and spacecraft icon/map are missing. They appear correctly on rerun, but 'suddenly' as described above.