You show the coordinate system for the layers, but not the scenes. In general, it has been the opposite that I have seen with regards to video cards. The Nvidia cards seem to not have issues, where as some of the AMD/ATI cards do. I would be curious to see if you have any vertical exaggeration set and what the coordinate system of each scene is. The coordinate system of your layer is meters based, so your coordinate system should be as well.
When you select the extrusion, are you selecting the minimum height? Or are you selecting the Base heights? Could that option have changed without notice?
I would encourage you to create an Esri Support incident in order to have someone take a look at your file and sxd directly. The only other test that I can think of is if you try ArcGlobe, will the extrusion still not work on the problematic machine.