I figured the only definite way to avoid parasites in the prey items was to just start a parasite free colony of my own with dewormings and all. Unfortunately that isn't an option at this point.

Parasites are very common, and I imagine that most wild BPs do have some degree of infection. Rats and mice are notorious disease and parasite hosts. My guess is that the BP's (or any animal) immunity takes a hit due to something else, and as a secondary complication the "normal, self-limiting" parasites take advantage and now become a serious problem.

Thanks everyone for the responses, it's nice to hear from the veterans about this!