Hi Eric,
This behavior seems to indicate ADMS performace issues, where large data sets (assemblies) will report false Vault status, such as not added, but if you open a smaller sub-assembly in the same Inventor session it will resolve correctly as Vaulted.
The best resolution here is to looking at defragmenting the database through the ADMS console, if you are running full SQL the advanced configuration guide will take you through a whole database maintenance plan which will typically help resolve these issues. Overall server performance, defragmentation may also help to a degree.
Changes in the Inventor add-in means that this issue is typically resolved in the 2009 release and beyond.
Hope this helps,
Allan (Autodesk)
Allan
Product Manager
Autodesk, Inc.