This is my guess: when you do a search for a food using the all foods tab, it uses data that is in a very large database. That database contains a lot of information, much more than the nutritional data that's posted on the side of a package.
If you use a lot of custom food information (I put a lot of custom foods in my log), it's going to use only the information that you can give. But if you also have food from the large database (for example, 'butternut squash, baked, with salt'), fitday takes all the information it can possibly pull from the database and can use it.
So the record of your nutrition is going to be incomplete just because the nature of recording your foods. If I put a kind of bread in my log, given what the package says, it's not going to record any pantothenic acid because that's not required to be reported. Some products will report this on the package but not all will.
So that custom food information gets counted with my nutritition, but any panthothenic acid is left out because there wasn't any to note.
Yet, there are items in the 'all foods' database that will have that. So they get counted and so show up on your nutrition report.
If I understand your question correctly (and I may not have!), that's my guess.
By the same token, looking at an individual food's nutrition info from the data base, not all information will be used in all displays.