Similar thing happened to another guy on the forums, with dragons. Do you have a lot of animals? Because there's a cap that can stop eggs from hatching and kids from birthing. Of course, check the hens. As previously mentioned, egg size affects how quickly they hatch, but it should be the same amount of time to hatch as the first batch.
That would be me! Things I learned the hard way:
1. Egg size doesn't matter. I played around with modding the egg size, it does nothing to the hatch time.
2. Animal cap matters. If you've got a lot of animals (more than 100 or so, I don't know the exact cap), try butchering the useless ones.
3. Make sure your food stockpiles don't allow eggs! You want pets, not omelettes. Your dwarves will steal the eggs if you aren't careful.
4. Make sure you aren't training the mother. The trainer will move her off the nest box, inadvertently killing the eggs.
If it's been a long time since the eggs have been laid and they still haven't hatched, do the following:
1. Deconstruct the nest box.
2. Dump the eggs.
3. Re-build the nest box.
4. Wait for the mother to claim the box again.
5. Immediately seal off the room with the box and don't open it again until the eggs hatch.
As a side note, if you are trying to hatch exotic animals, make sure they have all the right tags (like the [CHILD:1] tag). Compare to chickens or alligators to get a good idea.
Hope that helps!