This issue has been addressed in the following release:

Enterprise Vault 9.0.4
http://www.symantec.com/docs/TECH147785


Workaround:

To fix this issue you need to perform a Full Reset of the users Vault Cache by following this TechNote http://www.symantec.com/docs/TECH71311

However  the users may have un archived items in their Virtual Vault and if you perform a Full Reset these will be lost, so if required here is a full workaround for this issue

1. Close Outlook and take a copy/backup of the local cache folder (C:\Users\Username\AppData\Local\KVS\Enterprise Vault\*vault id*)
2. Open Outlook and look at the search folders in Virtual Vault and locate the pending archive items in the "to archive" and "could not archive" folders. 
3. Copy the items from these search folders back to Outlook but ensure you copy them based on folder structure as if you select all they will copy to one folder and lose the original structure.
4. Perform the Full Reset of the Vault Cache based on http://www.symantec.com/docs/TECH71311, then allow all content to be download again.
5. Once the initial synchronize has completed you can move the items back into Virtual Vault and perform another synchronize.