When the computer starts, Munki looks for a file called “/Users/Shared.com.googlecode.munki.checkandinstallatstartup” and runs immediately if found. When it’s done the file is removed.
As you could infer from this, the kickstart process is designed to run once — for example to get everything installed right away after bootstrapping a new machine.
If you do want it to run on every boot you could make an outset script that touches the file on every boot, essentially achieving the same thing as reinstalling the kickstart package on every boot.