For those items that are pending, can you find them in either Archive Explorer or Search.asp?
I've seen issues (rarely however) when the user is using Cached Mode and it doesn't update the message properly with the shortcut, so it looks like its pending, when really it has been archived correctly. You also see this in OWA where you have to hit the Send/Receive before it will go from Pending into a regular shortcut.
Other than that, if its just a few items, you can try performing a Cancel Pending through the client and then re-archive, as its possible that something had gone wrong archiving the item, you would normally see a warning in the Enterprise Vault logs where it says that a pending operation was cancelled
https://www.linkedin.com/in/alex-allen-turl-07370146