[eluser]Jeffrey McManus[/eluser]
I just thought of one more thing to try that pretty much confirms my assertion that this is an issue with CodeIgniter 2.1.x rather than a configuration issue or a problem with the data.
I grabbed a copy of CodeIgniter 3.0-dev from Github, configured it to work against the same database, on one of the same dev machines were I saw the problem last week.
Display of the data works correctly in this scenario. So from this, it's clear that between 2.1.2 and 3.0-dev, something changed with the way that unicode data is being handled. PHP/mysql does it right, CI 3.0-dev does it right, but CI 2.1 does not do it right.