I am the support technician that helped you through this. [-8
Just so anyone else looking this up knows the resolution, here's what we did:
Instead of using Provisioning we made a batch file that was able to handle reboots. The instructions for doing that are found on page 25 of the document found here:
We added the following lines to the end of the first batch file:
sdclient.exe /onreboot /bat /p="Name of batch file to run" /cmds="Parameters"
This forced the client machine to reboot, but then picked up with the new batch file after that. The document also shows how to run that all in a single batch file, rather than across multiple batch files.