I updated my Kindle to 5.1 a few weeks ago.
I just tested your issue, adding two old .mobi files I have (neither from Amazon) in
Calibre. Both transferred the Kindle just fine, appearing on the first Menu page of the kIndle (
most recent sort), with NEW tags, just as it should be.
I suggest restarting your Kindle. If that doesn't fix the problem, then a Factory Reset.