I've had the same issue once or twice on my XP system.

Mind you this was before I put XP SP1 on, so who knows, I've not need to sync since, so it may be busted now [like lots of things are with XP SP1].

I use Ethernet - a Dlink 10/100 mbs Etherswitch.
I've never used USB for this.

I also run the latest 2.0 B13 software plus Hijack [newest or pretty up to date at least] versions of software, and of course my emplode if B13 as well.

I did find that restarting Emplode did "reconnect" correctly & sync up again ok.