Bay 12 Games Forum

There must be something wrong in your setup somewhere. Eggs are laid unfertilized if there is no chance for them to be fertilized. For instance, if you plunk down your nest boxes and then lead the bird into the pasture the females will generally lay eggs immediately without giving the male a chance to fertilize them (at least that's my experience).
A DF change about half a year ago changed the rules for fertilization from teleportation (anywhere on the map) to proximity, so the two (animals or dwarves) have to be next to each other for fertilization to take place.
Thus, if you separate males and females into separate pastures you'll get eggs, but not fertilized ones. A huge pasture reduces the chance of the two animals encountering each other and thus fertilizing them.
I'm not sure about this, but I also suspect female birds will lay eggs immediately when matured if given the chance, in which case the eggs probably won't be fertilized. Also, it seems birds will usually lay a new clutch of eggs immediately when the previous one hatches, and again, that might leave little room for fertilization in between.

My bird raising strategy is basically to build a pasture, lead the birds in, and then plunk down nest boxes. I then forbid one clutch of fertilized eggs from each kind, while all other eggs are collected (hopefully, I suffer birdsplosion from time to time). When the chicks have matured I slaughter off all but two of each gender and select a new clutch to mature. I also use a variation of this, by having small (3-4*1) pastures with a nest box where I place the two breeders and I then lock the door to block egg collection. I then check for eggs periodically, and if they're unfertilized the door is unlocked until the eggs have been collected, after which the door is locked again.
Note that the above provides lots of eggs that are collected without any check for fertility for most of the time.