I've put a new test build of the GUI version of JHOVE at (http://jhove.sourceforge.net/JhoveView_4-Sep-2012.jar). This addresses one of the most persistent problems: the configuration file. If it can't find the expected configuration file, it creates a default version.
I've tested this on a Mac and an Ubuntu box, but not on WIndows, which is the toughest case because of its different and changing file system conventions. I'd greatly appreciate feedback on whether it works right on Windows, and which version you've tested with.