Figured out how to recreate this every time. If you do a save as and select advanced and rename the components in the assembly, but don't rename the top level assembly, then the first part in the assembly becomes a multi-body part with all of the assembly components and nothing else gets saved. It all looks like it worked and looks fine until you open the 1st component in its own window, or try to open one of the other components and it will say in can't be found. Turned this in and I believe it is fixed in 2015. Sure hope it gets fixed in 2014 SP5!