The Advanced Run Options "Throttle inventory scan evenly over a priod of: X hours" extends the execution time of the policy. Reboots, log offs, etc., can interrupt the inventory execution, causing it to fail.
Try removing or shortening the throttle time. Make sure the time does not extend to past the end of the working day where users will turn off their systems.
Splitting the Inventory policies into different groups can achieve the same affect and lighten the load of Inventory arriving at the SMP Server.