We are seeing this problem also, I have recently installed the CP patch but 1 in 3 systems will still fail from the reboot task at times. The current system I am working on is failing at the reboot task only after the agent is installed. However the reboot tasks before the agent is installed are working ok. I replaced the reboot task with what elkum suggested and used execute file. This is sorta like the patch system task that does not work in 9.5 however if you use execute file and use vulscan /repairgroup then it works. I will let my system build over night and add my name to the fix request with support tomorrow if this is still not working.
EDIT: Provisioning template was a success after using execute command for reboot step after the agent is installed.