Glad its working! As I'm tinkering with a few different MoodleBoxes, I often change the SSID myself. I also enable https first thing to make connections a little easier. One of my common problems, I end up thinking the MoodleBox Wifi password is the login password, and keep typing in the wrong WiFi password.
I'm going to speculate, but guess my speculation is incorrect: If you were on a MAC in a terminal session, and had ssh'd to the MoodleBox, then done a shutdown from the web interface on the MoodleBox. Your terminal session might have then been on the mac, and it wouldn't have found that file. Anyway, I know I'm probably wrong, as you mentioned you'd changed the directory.