I am creating an RCP application, with many Greek messages, so everything is in UTF-8. As I develop and test through Eclipse IDE, everything is fine.
When I am deploying
(copied from the question - so this shows as having an answer)
I found the solution although it was not as trivial as I anticipated.
Eclipse gives the ability to control the build process with build.properties, in which you can specify a property javacDefaultEncoding with the following value for example
javacDefaultEncoding..=UTF-8
Documentation can be found at Eclipse Help in "Plug-in Development Environment Guide > Reference > Build Configuration"
Hope this helps someone.