Hi Scott,
This seems to be a procedural issue as you suggest with your designers manipulating their local copies instead of using the latest Vault copies.
There is a number of reasons why we retain local copies of files but are aware of the issues related to working on older copies and have implemented a number of tools to remove the likelihood of users checking in incorrect files.
1. Close and delete files on check-in: this option available on check-in allows users to remove the existing copy of the file once they are done with it.
2. Workspace Sync: Vault Manufacturing allows users to scan their local workspaces to update and/or remove out of date design files (Managed and unmanaged)
3. Check-out rules: any out of date files will NOT permit check-out operations preventing users from modifying the wrong version of vaulted files
The most important thing the users can do here though if there are rapid changes being made to the designs the team is working on is simply to NOT open the local copy but open the drawings and assemblies directly from Vault.
Using "Open from Vault" command will ensure they always have the latest "checked in" version of the file for modification.
Moving and renaming files within the Vault will also require this same dilligence - moving a file in the Vault will create a redirection link in the assemblies and drawings but does NOT move local copies of the data - these need to be removed before or after the move command as do renamed files (Workspace Sync is great again for this).
In terms of file status icons this is a different matter - I would suggest opening a support case with your reseller if the file status icons in Inventor are not reporting the file status correctly, this is a little curious.
Hope this helps,
Allan (Autodesk)
Allan
Product Manager
Autodesk, Inc.