edited a couple time after some tests
Eclipse's encoding is set in
preferences->general->workspace, which whould by default be inherited from the OS (cp1250 on windows).
When you create a "Run as" task, it also stores it. So if you update eclipse's setting, make sure you re-create your "run as" task. You can see the actual value used when launching your application:
Run configurations... -> Your Run task -> Common tab.
You can also force an encoding in eclipse.ini by adding
-Dfile.encoding=AnotherEncoding at the end.
When launching from the command line, it takes the system default value, which would be cp1250 on whidows.
You could print the encoding at the very first line of your program, just to see:
To specify an encoding from the command line:
java -Dfile.encoding=UTF-8 yourApp.jar
Take a look at this too: http://stackoverflow.com/a/14867904/641627
This indicates a problem with your code. Your code is currently depending on the default platform encoding, and doesn't work if that encoding is not "UTF-8". therefore, you should change the places in your code which depend on the default platform encoding to use the "UTF-8" encoding explicitly.