I have attached a couple of shapefiles, one has 156 polygon features, and the other has 157 linestring features, and this is pulled from a data set containing a few million features. I have been unable to figure out which tool/operation within Openjump that will allow me to compare two layers and extract only those geoms that are different, and I have been unable to successfully use just a simple Delete Duplicates operation.
In the 157 shapefile, I denoted which feature is duplicate(under notes column the record named 'duplicate), but I denoted this manually, as I was unable to identify it using any of the operations that I thus far understand within OpenJump... I would've thought that at least the Delete Duplicates operation would have worked, but it did not, so perhaps it would work on a Windows version? Without looking in the attributes, see if you can use Delete Duplicates to identify the problem feature, because it would not work for me.