Well, you're all right ... Java uses unicode internally but uses the local system encoding when reading/writing files. I had to explicitely set the encoding to UTF-8 when reading & writing the files, while I thought the XML encoder took care of that (I set the 'encoding' property to 'UTF-8' and thought that was enough ... that was clearly not the case).
Like I said, I should have tested this thing more before releasing it. It was a simple app ... and the xml files looked OK (in notepad) ... no need to switch on my iLiad, it would work anyway ...
v1.3 should work completely (and I tested it quite thoroughly - on my iLiad), you can find it on the first post as usual.