I couldn't find a bug report for this -- the eggs are supposed to last a week unattended, the egg-sitting behavior is fairly high priority, and the timer resets if there is any sitting at all, so minor disturbances shouldn't matter. I don't have a lot of in-game experience though -- does the weekly timer seem to be broken? Or do they not go back to their box?
I believe there is some confusion over how egg laying worked exactly (I didn't know there was a weekly timer, and it isn't mentioned on the wiki). There are a lot of variables involved, mainly due to whether or not the eggs are fertilized. It is hard to tell if the eggs failed to hatch due to an egg-layer with insufficient time on the nest box, interruption by other creatures, or because the egg wasn't fertilized in the first place. I was under the impression that the bird needed to stay on the nest box the whole time, and no creature could ever be on the nest box other than the mother, or the eggs would never hatch. However, I vaguely remember seeing an elk bird move off of a nest box (for training as I recall), thinking the eggs were ruined, then seeing them hatch anyway.
The concern is that you'll need males close to the females under the new system, and current approaches to handle the confusion (I'm looking at you, Incubation Chamber on the wiki
http://dwarffortresswiki.org/index.php/DF2014:Nest_box) don't have them present. It's hard enough to tell if eggs are fertilized as they are now (you essentially just wait two seasons and hope something hatches), and it seems that it will be even harder in the future when you also need males (who may not even be interested in the females according to
http://www.bay12games.com/dwarves/mantisbt/view.php?id=7651) nearby. On top of that, short times between eggs collected / hatched and laid would seem to make it difficult for the males to fertilize the eggs.