Just to confirm - is this when using an agent, using the "Run on boot if schedule missed" option?
No i am not running a agent
Where are you setting up to run at next startup then? The only option I'm aware of that is available for agentless patch deployment similar to this is the "Install at next reboot" option.
I can tell you that if you are using agentless patch deployment it will be using a scheduling method to set up any scheduled deployment. The scheduling method is set within Tools > Options > Scheduler. Click 'F1' while in that screen to get the help file about the scheduler settings.