I have noticed that SQL Agent does not start automatically after a reboot/shutdown on a few of our servers (SQL server starts up fine). The service is set to automatically start in windows. When we start SQL agent manually, it starts fine.
Add your windows level user in following path:
Click on Start - Run - Secpol.msc
Go to: Local Policies - User right assignments
Ensure the user account your running the SQL Agent Service under has the following assignments:
Act as a part of the Operating system
bypass Traverse checking
Lock pages in memory
Log on as a service
Log on a batch job
Replace process level token
If not, please add them and try restarting your system. Your SQL Server should be now be automatically starting as a service.