This problem just started for me today. I bought a new Contract to gain extra rep with Assembly of the Deeps, but to my shock and annoyance, when I did ANY WQ, I got only reputation with my guild. I did both pet battles and regular combat quests, and neither gave me rep with the local area (Council of Dornegal) nor the Contract party (Deeps). The Contract is active on my buff bar.
(I double checked to see that my chat had Reputation Gains on, and verified by looking at the reputation numbers in the rep overview. The numbers didnt change)
If there is no rep, there is no point doing WQs… so I hope this gets fixed asap.