it's rather hard to make one config file with many purposes... I18N of the webapp should be done in the java way, with property files and MySQL has nothing to do with it. Besides that, most config items are in one place (jbpm.cfg.xml)
Instead of these very generic comments, I'd appreciate some (not all) detail so I can get a better impression of the issues you ran into. I my self have not had any issues between e.g. Linux and Windows.
If you want to contribute, we'll be grateful, but it is better to take part in redesigning the console to Seam. The current one is rather difficult to maintain.