Eric,
Attached is a zipped folder containing a file geodatabase that includes the multipatches I want to union (Multipatch 1, 2, and 3). I was able to merge 1 and 2 (Multipatch12_Merge) and then union 3D them (Multipatch12_Union). I then merged this last feature with Multipatch3, made sure they were all closed, and then tried to union them. This is when ArcGIS crashed again, and so I am not sure if it is at this point that ArcGIS crashes.
Thanks for your help,
Winn