The problems people had around the end of last year when installing samples were confirmed as a firmware bug that has long since been fixed. I haven’t heard of anyone having that particular issue since the 2.1 firmware was released, so I doubt it’s the same issue.
I have, however, seen one other report of a problem following a 2.1.1 beta that sounded similar. Write to Sequential support and I’m sure they’ll get you up and running - they had no trouble resolving the issue with a quick support call the one other time I’m aware of. The latest updating instructions indicate that you should wait ten seconds after the Prophet X finishes the update and asks to be powered off and back on. That suggests that there’s a known issue with powering off too quickly after an update. Is there any chance this was the case here?