My Black headed python used to do exactly the same thing. I posted a thread about it way back when, but i got no definite answers. The snake did NOT have mites.
The snake would shed, or seem to be shedding pretty much all the time. Apart from constantly having really wrinkly skin and cloudy eyes all the time, the snake seemed very healthy and fed regularly. It was quite stressful as the snake looked terrible most of the time and i was worried something was seriously wrong. This went on for a few months.
I took it to a vet one time, but i got no real reason as to why this was occurring. Eventually i put it down to a humidity problem and swapped his larg-ish water bowl for something smaller. Ever since i did this, the problem quickly stopped.
However, in hind sight, i had another thought that began to develope. The larger water bowl had originally come with an adhesive sticker on the inside of the bowl (where the water would go) that was very hard to remove, and although i got off all the adhesive i could, there still appeared to be slight remnants that would not budge. In my mind at the time, i thought surely a pet manufacturer would never use a harmful adhesive on their products, especially for water bowls. Needless to say, just tp be on the safe side, i dont use that water bowl any more for any of my animals. Maybe this adhesive affected the water just enough to cause skin irritations when drank or swam in...
Anyway, i guess you could say i have no difinitive answers, but as this same problem once happened to my snake, i thought i would share everything that i knew about it. It may be the humidity, or perhaps some sort of chemical that the snake is exposed to. Of course, it could be something completely different.
Hope you can work it out mate.
PS - I did a bit of searching and this is the thread i started when i had my problem. No real answers lie within, but thoought it might give you something to work with.
http://www.aussiepythons.com/forum/australian-snakes/the-shed-a-thon-84346