Storage question on iPhone 5s

I have a 16 GB iPhone 5s that says it has a capacity of 12 GB (As a side note, my 16 GB iPhone 4s has a capacity of 13.6 GB so I'm not sure why the different iphones have different capacities on the "about" page). Running on iOS 8.2 here, I went through and added up the storage to every single app I have and the total came out to be 9.5 GB. That means that I should have 2.5 GB free. Instead I have 110 MB free.

Before people come in here and tell me to delete text messages or use a program like phoneclean to delete app data and such, remember that this 9.5 GB includes a catagory called "messages" and all the app storage includes "documents and data" storage inside of it.

So, where is this mysterious 2.5 GB? Do I have to do a full restore to get it back?