James Hardi backer board made in Mission Viejo, Ca is some good stuff. Its make of stuff that does not do the things you are seeing. It will almost sit in water and not cause problems. I personally use it allot especially when customers having problems with original wood siding rots where it touches the ground, perfect application for hardi board.
I too think you are seeing something else. T-111 will do this when not kept painted, Masonite siding will do this if the edges are not caulked properly.
Hardi has only had problems with their shingle material and they fixed that last year.