If those two lines of code produce different output, that's because they have different inputs. So
you should start looking there.
I'm a bit confused because I don't understand a lot of things in your post. First of all, all
Java characters are Unicode. They all come from the Unicode character set, which includes ASCII as the first 128 code points. Probably you meant that you have some non-ASCII characters.
And I don't understand what it means to "display as unicode". I don't even have a guess for that, so perhaps you could provide an example.
And this console: is it the Windows console, or the Eclipse console, or a Unix shell? They all have different behaviour.
As for MySQL, when you set it up did you configure the database to use UTF-8 as its default character set or did you use something else? UTF-8 is a better choice if you're going to have international inputs.