There is no plausible explanation why it should sound louder. In order to add loudness you would need to add MSB (most significant bits) to the data being read from the CD. This would also require changing the appropriate bits in the error correction formulas that are embedded along with the music data in the stream of "pits" read from the CD by the laser (so that error correction still worked). The probability of this happening in such a way as to uniformly raise volume from cleaning a disc or marking it somewhere is fairly remote...a lot less than winning a national lottery.
This suggests that wishful thinking goes a long way. In medecine they call this the placebo effect. In psychology students are taught that you see the world through the framework of your mind and you can choose to predispose your mind to be optimistic or pleased about things or to be morose and unsatisfied with things. In this manner, exactly the same situation can be perceived differently by the same person, depending on the how the mind has been predisposed. With some training you can teach yourself to select the optimistic view of things (glass is half full) and to recognize when your mind is predisposed to react to inputs in a negative fashion. In simple terms, this is like taking the "Mary Poppins" attitude to things....everything is fun, even work.
Another explanation, perhaps a better one, is that if you stop the music for a minute to mark your disk then your ears/brain will adjust to the silence....then when it starts again it will sound louder (initially), as you have just been accustomed to silence. Musicians and composers use this all the time with great effect...a quiet passage before a loud passage helps to add contrast and make the loud passage appear louder than if it were not accompanied by a quiet passage.
Just two cents...I don't want to spoil your illusions but this kind of thing is part of the reason that testimonials are not trusted in science unless they can be shown to be statistically meaningful under double blind conditions...the mind constantly adjusts and alters our perception.
