Hello Liam,
I believe you are in the right track, I have seen other users loading the sketches into the shell. I will try to get more information about the USB port behavior in the meantime please verify this discussion, https://communities.intel.com/message/223241#223241 , it will give you useful recommendations if you want to run the sketches in Linux, If I find more information I will post it in this discussion.
LDiego.