I am not truly certain how to explain this issue further except with a bunch of photos.
I am using VaultChatFormatter (because I thought the problem existed only within EssentialsXChat) with the following format: format: "{prefix}{name}{suffix}&7:&r {message}"

I have configured prefix stacking to work as such:

  prefix:
    format:
      - "highest_on_track_staff"
      - "highest_on_track_donor"
      - "highest_on_track_local"
    duplicates: first-only
    start-spacer: ""
    middle-spacer: " "
    end-spacer: " "

And the result, very visibly incorrect is this:

The local track:

And some debug output: https://hastebin.com/raw/inamibefic

As a note, this issue is not present if the prefixes exist in a global sense, rather than a specific server context.

Output of /lp verbose after a bit of checking: https://luckperms.github.io/verbose/#3sZPlKmyUn
Some things to check out:

vs

Which shows that the check from vault is not maintaining the same contextual information as the check from the plugin itself.

Make sure this option is set to false

https://github.com/lucko/LuckPerms/blob/c7a0d7026c9122292b33c8f1ea445cf0eef9201a/bukkit/src/main/resources/config.yml#L504-L507

Failing that, double check you're using the latest version. (it looks like you are already though)
https://luckperms.github.io/

The configuration was outdated. These options were not present. However, the issue is fixed after migrating to a new configuration file.