Without knowing exactly what this pet bedding is I can't say if it's the problem or not however I can make a few guesses. One way or another your snake's skin is getting some sort of assualt, be it bacteria/fungi growth or dampness, or acidity ect. The most common reasons for this type of problem go hand in hand. Them being cleanliness and humidity.
I recommend a total reevaluation of your enclosure and husbandry. Ask yourself the questions... why was my snake previously not using a hide box. Am a changing the substrate often enough? Is my humidity too high, should I be provide both a dry and a humid area? What is most suitable for this species of snake? Is my temperature gradient adequate and is it easily utilizable for the snake? Does my snake feel secure in it's enclosure or is stress/exposure a problem?
If you need any help with these questions, feel free to ask, and don't stop with this short list.
If you don't see improvement after the next shed, if there is a problem with the next shed, or if it gets worse in the mean time, take this critter to the vet and have it examined. For now, a quick and gentle wash, rinse and dry with antibiotic soap (dilute chlorhexadine or betadine) might help things in the right direction.
Good luck!
Ian