I had this same problem today. I updated to 3.0.0 recently, everything worked fine. But going from 3.0.0 -> 3.0.1 my Helix was stuck on the "update message server started" screen for about an hour. The "installing" progress bar in HX Edit never showed up.
I killed the HX Edit program, cycled power on the Helix and it booted up back on 3.0.0 just fine. Repeated the update process and now 3.0.010 is working. Not sure how risky that is, but it looked like the updater process hadn't actually started yet so I figured it was OK.
