Paul, the usual way that things have to be restarted during runII is to wait for a run to end, turn off the modulation (make sure to wait till it is finish exiting in the TS0), reboot the TS to make sure the laibraries are properly reloaded, when the TS is back click restart a few time on the GUI, and then turn it back on. Normally this all take a few minutes.
This seems to be the only reliable way to restart since run II started.