The names of places and transitions displayed can be repositioned by dragging with the mouse and the resulting positions are saved in the xml file. (<name><graphics><offset>). However, when reopening the file the saved positions are ignored and offsets revert back to 0.0. Hopefully this is a simple fix.
BTW, great job fixing the most annoying bugs from version 3.
One thing that would be nice is if the examples could be updated so they would open without error. It seems to be all associated with the addition of the <token id="Default"> tag and references to it in the <place><initialMarkings><value>. When I edit the example xml files and add those then it can be loaded.
Fixed in version 4.2.1. This was indeed an easy fix. The variables were being passed into the proper methods, but the constructor just wasn't doing anything with them.