I didn't think Empackager allowed you to type anything in the debug window. I think it's just to see/copy the text for debug reasons. You shouldn't have to reboot the empeg yourself at all during the installation. Empackager should be started with the player already running on the empeg, as the first thing empeckager does is send "q" to the empeg, thus quitting the player.
HTH,
Jason

_~= Dearing =~_
"WAY too happy about having #99."