Forge: forge-1.12.2-14.23.5.2838-universal
Sponge: spongeforge-1.12.2-2838-7.2.1
LuckPerms: LuckPerms-Sponge-5.1.17
LuckPerms config: https://gist.github.com/pinkpig3777/96ab67db14d3e2dbbb3822e84fdb3495
latest.log: https://gist.github.com/pinkpig3777/62fb57dff93e24f845b1d3e0e30e1d52 (Server crashed shortly after but that is unrelated to the problem, although if you do see why please LMK)
debug.log: https://gist.github.com/pinkpig3777/21c450fdd1b713f4bf445f852b1708c6

Issue:

• The prefix the user has is not consistent with their actual rank.
• I believe this is due to this section of the config being broken (probably suffixes too, I didn't test):
  meta-formatting {
  prefix {
  format = [
  "highest_on_track_builders"
  "highest_on_track_staff"
  "highest_on_track_donors"
  ]
  Specifically the "highest_on_track_" feature (others may be too, not sure).

The Bug is best explained in an example:

• Let's say my Staff track consists of "Mod", "Admin" and "Owner". And I am set to Mod rank. The LuckPerms config is set to show the "highest_on_track_staff". Thus I should have the [Mod] prefix because that is the highest rank I am added to on that track. However, what it actually does is show [Owner].

In the following picture you can see a similar situation, but the track consists of:
....., Admin, ....., Owner ranks. In the picture I am always Admin rank. The only thing that changes is at first it uses "lowest_on_track_staff" then I change it to "highest_on_track_staff" and reload the config.
https://gyazo.com/818d50e4fa55258c75ad62526d57acf0

Well, figured out the issue. My inheritance was messed up.