I only know of one X11 change that occurred between 9.4.1 and 9.4.2, which is !11985. Though I don’t see why it would cause any problems for Xvfb.
@bfosso, if you’re using Python, can you do a trace (e.g. python3 -m trace someprogram.py) to find out what VTK method is called immediately before the error occurs?