a blue poster has acknowledged that they are aware of the bug, but currently do not have an ETA on when it will be fixed:
"While I don't have any information available I can state that our QA team and Development are aware of this issue affecting some people. They are looking into and hope to have a resolution implemented as soon as possible."there's no work-around that i know of at this time, but i'm hoping one does come up if blizzard cannot fix this devastating bug before the in-game event is over.
i don't know about everyone else, but i'd like to know why a bug like this has reared its ugly head all of a sudden. it was pretty easy to pinpoint the cause of the northrend orphan bug; the quest timer was simply not reset in time for players to complete a second time. however, unlike the nothrend issue, both stormwind/ogrimmar and shattrath questlines have been pretty stable in previous years, and nearly all players have been able to complete them. was it the major changes to this year's quests? that doesn't explain the shattrath bug, though, as it did not receive any update (other than the addition of a new pet reward) that i'm aware of. why is this bug afflicting only some and not all players? does it involve certain phasing, perhaps?
in any case, my heart goes out to my fellow pet collectors that are suffering from this issue, and i absolutely hope that it is resolved in time.
UPDATE: the thread linked above has been updated with a possible work-around. try destroying the orphan whistle and talking to the Matron to receive another one. hopefully that will help unlock the rest of the quests. understand that this may or may not work for everyone.
UPDATE #2: if the above work-around doesn't work for you - "If the final quest in the Children's Week line for Azeroth or Shattrath has not reset, so you are unable to obtain a pet, please submit an in-game petition. Make sure you do the other quests leading up to the last one, a Game Master should be able to assist you to manually complete the quest."