So I had 457 Reputation with the Amalj'aa, (friendly) then handed in 6 quests which should have brought me up to 508, and they actually TOOK AWAY 49 points bringing me to 408. 100 Reputation points gone. I contacted Customer support, did a in-game bug report, E-mailed Square Enix and even talked to a GM in-game. They keep sending me in circles back-and-forth-back-and-forth. I did one quest for the Amalj'aa and that one worked normal, but afraid to do any more quests in case they keep taking Reputation away from me once I get to the 510 mark. Less then 100 points away from a mount to boot. (I think)

Started with: 457 Rep
Completed 6 quests: (Should be) 508 Rep
Ended with: 408 Rep
100 Points GONE.

I have no other option but to keep E-mailing Square Enix until they restore my 100 points. In the meantime I guess I'll just...