Based on the most common form of this, persisting sensations, I came up with the following 'theory'.
My theory is that after the brain has received a given input for an extended period of time it will, if it 'considers' it 'unimportant', stop 'making' you conscious of it. However, when the input is removed, it now 'expects' an input that isn't there. Due to this irregularity your subconscious now 'makes' your conscious aware of this by 'sending' the 'signal' it has not been 'sending' previously. After a time of no input, your brain adapts and stops giving this signal.
I've stuck a load of apostrophes around words there because of the difficulty in describing concepts like this. I believe this description is easier to read this way. However, one can see how this could genuinely occur in the brain.
This 'theory' is possibly thrown off by the fact that these persistent sensations also occasionally occur long after the input has been removed. Any thoughts?