Farmville has just admitted what many of us figured out - parts for nurseries, Japanese barns and probably for stables are just disappearing. You add them, you can see them in the structure too. But the next time you enter your game they are not there! They go to Farmville heaven I guess. They claim they have "fixed" some of the problems. Maybe, Maybe not. The problem appears to be much worse if you are building 2 or more buildings at the same time.
A suggested work around: Gather all the needed parts first. Transfer them to your gift box but do not put them in the building until you have everything that is needed. Then put at least one animal in the building to make certain. Once the building is completed, and you have some animals in it, it seems unlikely that farmville will stead parts from you.
Farmville says that "critters" are also disappearing. I wonder what that's about, and why their messages have to be cryptic!