What version of code did you upgrade to.....and from?
Without more information on your issue, I'd just confirm the following: The release notes for the newer releases outline the upgrade paths from older versions. In some cases you need to perform a hop upgrade, for example anything earlier than 5.0.3.1 needs to upgrade to 5.0.4.x before going to 6.1.x. If you don't, you'll get a variety of error messages (not sure if this is one or not).
If this was the case, then just flash the same image again and see if it resolves the issue.