The error parser cannot handle absolute file paths, even if the sources are located in the project. The complete absolute path is always appended to the project dir and the working dir. I tried to fix this with my very poor java skills in the latest svn sources, but the snv is too old (1.1.5) so the preferences save bug is still unfixed.
Can anyone of the developers provide the source of the current 1.1.7 for further development?