I saw this post from a few years ago. It may help. batch package with reboot
Looks like they were able to get the reboot to continue using the 'sdclient.exe /onreboot /bat /p=...' Still had a problem with the machine not running the 2nd batch when the user did not immediately logon to Windows, but this could be done with a registry setting to AutoLogon. At the end of the 2nd batch file remove those registry settings, and reboot once again.