After upgrading to 962 I uploaded a new PKG to the JSS and set it to install at reboot, and added it to my workflow. What I noticed was that when I netbooted a machine, and selected the workflow the PKG I added stays under the first stage of the imaging process. If I click refresh, then it appears in the post-reboot section.
I also noticed in earlier 9.6 versions that I can't seem to install any PKG files during the first stage, they all have to be install at reboot.