How did yo put the files into the Vault in the first place?
If you did "Add Files" from Vault Explorer, or a drag 'n drop, all you did was add the files into the Vault as file objects without capturing the file dependencies. This results in the behavior you have described. You should have recieved a warning message about this during the add files process. "You are attempting to add Inventor files... relationships may be lost". This method should only be used when adding files that have no dependencies.
When loading Inventor files to the vault it should ALWAYS be done from within the Inventor environment. For just a few files, while they are open in Inventor, change to the Vault mode in the browser, (you'll see ?'s next to the files not in the vault) RMB on the browser & "Add Files" This adds them to the vault w/ all relationships intact.
To load large batches to the vault without opening them, from within the Inventor environment File>Vault>Add Project. This will read all of the files in the workspace of the active vault ipj (plus any mapped libraries) into the vault complete with all relationships. This is the most common method to do the initial load of files into the vault when starting out.
Again, when loading Inventor files to the Vault, you should always do so from within Inventor & not from Vault explorer. Only in this way can the file resolution dependencies be "read" into the vault. Once there, vault can manage them very well.
Personally, I'd start over from scratch and reload the stuff to vault. Read up on how to setup etc (Managing Your Data) and be sure you understand how Vault handles different types of files. Be sure you back up your data before starting so you don't lose anything.
To get back to where you started before trying to use vault....
1. Retrieve the files from Vault, From Vault Explorer, "Get" everything out of the vault to the workspace (libraries to the library locations). "Use the "Get Entire folder" command
2. Change to Read Write. Once all files are copied back out of the vault to the workspace ( & libraries), use Windows Explorer to change all files from "Read Only" to Read/Write".
3. Clean out the Vault. Delete all of the Vault files to start over (or create a new vault). You are now back to the No Vault (pre-load) system you started out from.
4. Review the set-up. Check that your ipj is properly designed, with libraries planned etc. Check that the vault folders are mapped correctly(Inventor>File>Vault>Map Folders) This is ususally Root=Top Workspace folder & Library = Top Library folder and content Center files reside under this.
4. Load the Vault, From Inventor, with vault ipj active, Run "Load Project".
5. Set Workfolders(s), From Vault Explorer, highlight The top workspace folder (not $root), RMB set workfolder, choose the local top workspace folder. Do the same for the Top Library folder.
6. Test the system. From Vault explorer, get or check out a file with dependencies (ie. an idw/ipt). Test from Inventor, Get, Checkout or Open from Vault, a file with dependencies. It should get all needed files to your local.