It's not a bug. you buy the writs and then you go buy the faction tokens that give you 250rep each. when you use the, i think you get 25 rep for ALL cities.
Also, when you champion a city, you get 350 rep for each daily turnin (i'm pretty sure it's 350). IF you're still doing the dailies for them when you hit exalted, that 350 rep per turning now becomes 65 rep for each of the other cities.
One tip when grinding through the AT Dailies is, for the next city you champion, find the one with the lowest rep and grind it until it is close to even with the others. you can grind the same faction over and over, even past the 25 valiant tokens you need.
I know, my point was in the process of being champion with all five cities I somehow got around 6000 - 7000 rep with each city from doing valiant and champion dailies. So by the time I was a champion with all five cities I was also Exalted with all of them and I was sitting on 18 writs that were now useless. That was when AT started though, it seems that was corrected/patched out.