I just switched over to SW PDM and am in the process of moving some assemblies into the vault that used to be stored locally. The "Update References" feature has been excellent for redirecting the references from the old local location to use parts from the vault. However I just added an assembly file into the vault and ran the find references tool, but nothing was showing up. It had me confused for a while until I realized it is because my top level assembly just contains 2 virtual subassemblies, and each of those contains a bunch of parts. For some reason the find references tool can't see past the virtual subassembly level to update the part references. Sure enough, if I add a random part to the top level assembly so that it contains 1 part and 2 virtual subs, then when I run the tool only the 1 part shows up.

Any idea how to resolve this, or is it just a bug? 

The only workaround I can think of right now is to save the virtual subs to actual files, then update references, and then change the subs back to virtual and delete the saved files. This will not be a big deal with this particular assembly, but if I have an assembly with several levels of virtual subs then it would be a hassle.