Hi,
If some of your sites are sub-domains or sub-directories of other sites, then they will be grouped together under a shared folder in Vault.
Could you send us an example of some of the sites that are not showing in Vault?
If possible, please could you send a recent backup log from these sites?
The logs can be found in the UpdraftPlus Existing Backups tab.
The contents will be too long to post here directly, but you can use an online service such as Dropbox or Pastebin, and post the links here.
You can also set your reply to ‘private’ if you prefer.
Best Wishes,
David N