The functionality has only changed insofar as the PDFBox library used has been upgraded from v1.x to v2.0. The library itself underwent a significant refactoring however.
Based on a quick review of the code in /javasource/Misc.java, the module is using the setDefaultOverlayPDF function. PDFBox offers another method called setFirstPageOverlayPDF. I'd recommend you first try just changing the method called and see if that works, and then properly implement this by adding an option to the overlay Java action.
This turned out to be a conflict in a specific JAR file, see the thread:
So, if this is the case, remove 'pdfbox-1.8.5.jar' and rebuild the project.