Sounds like a bacteria growing from moisture. Try using bleach. Do you have adequate ventilation?

Strange indeed. I had to look up Pex to discover what you were referring to. Way down on the Wikipedia page it speaks of problems with iron in the water supply and radiant heating, but I don't think that applies to you.

Also discovered this link at the Terry Love Plumbing forum.

-Babka

Here is a link that might be useful: Orange stains (iron) with Pex

Orange staining is usually from iron in your water or it can be a type of algae. I'd get your water tested for iron, if it is high it's not harmful but you can get special filters to remove it to prevent staining. If it is algae, keeping things dry and using dilute bleach or hydrogen peroxide will help.