Hmm, You're avatar is pretty much me right now. So that article says partition gaps can be intentionally created and vice versa (unintentionally)? Doesn't really answer my question completely unless I'm missing something.
Let's see if I can unscramble your puzzle, are you asking for example if you had a 100GB hdd but it only shows as being 95GB? If this is the case it is normal, the hdd retains a space/cache in order to move information around.