I have discovered what the problem was, it was a conflict with the firewall (Tiny Firewall) on my desktop machine. The firewall software should have prompted me when emplode tried to connect to the unit and asked if I wanted to create a rule to allow it. For some reason it was not giving me this prompt. When I went in an added an explicit rule myself it worked fine.

Problem solved, now to see if Ethernet syncs are anymore robust using this machine that USB syncs are...