When you say:
"BSA does not seem to continue past the reboot", what does that mean? Have you deployed this package before on other servers, and with better results?
Are you saying the server isn't available (not polling) in the BSA console? If so, can you right click and refresh the server manually? Does it refresh when you do this, if this is the issue?
Also, are you able to determine if the Windows server is up after the reboot and the RSCD service is running?
open a ticket w/ support.