One of the things that has irritated me about the persistent USB thumb drive installs is the “Press Enter” to continue prompt on shutdown. Luckily, if you have persistent working correctly, the fix for this is easy.
Open up /etc/rc0.d/S89casper
Search for ENTER and the shutdown string “Please remove the disc and close the tray (if any) then press ENTER: ” > /dev/console”
For me, this was on line 89. Comment out, that line and the lines down to the ending bracket for the do_stop() routine.
Reboot, and see if you have that annoying message, if not you’re good to go.