The setting "Faction Tabards Reputation" does not work in old dungeons if you have the "Watch Subzones" setting also enabled. It will automatically switch to the standard reputation (f.ex. The Consortium) upon entering a new sub-area of the dungeon.

I've confirmed it's not an addon conflict because I turned on Verbose and this is the output:

[11:53:00 PM] Heroic - Tavarok engaged. Good luck and have fun! :)
[11:53:00 PM] Reputation with The Consortium increased by 275.
[11:53:00 PM] Reputation with Exodar increased by 330.
[11:53:00 PM] Details!: First Hit: [Judgment] from Ilyxiana
[11:53:01 PM] Heroic - Tavarok down after 0.00 seconds! Your last kill took 0.00 seconds and your fastest kill took 0.00 seconds. You have 4 total victories.
[11:53:03 PM] You receive loot: [Shaarde the Greater]
[11:53:03 PM] You receive loot: [Netherweave Cloth]x4
[11:53:03 PM] You receive loot: [Lightning-Rod Pauldrons]
[11:53:03 PM] You loot 6 Gold, 72 Silver, 43 Copper
[11:53:04 PM] You receive currency: [Spirit Shard]x1
[11:53:06 PM] RepByZone: Now watching The Consortium
[11:53:09 PM] Reputation with The Consortium increased by 3.
[11:53:09 PM] Reputation with Exodar increased by 5.
[11:53:09 PM] Reputation with The Consortium increased by 4.
[11:53:09 PM] Reputation with Exodar increased by 6.
[11:53:10 PM] Reputation with The Consortium increased by 3.
[11:53:10 PM] Reputation with Exodar increased by 5.