Sharp cracking sounds more like checks opening up in the timbers than anything, but the timbers are certainly done drying by now and it sounds like you have eliminated that option. Does this tend to happen under high wind conditions or a similar consistent variable? Does it seem to be localized on any particular side of the building? It would seem that if the panels were rubbing or flexing it would be more of a creak or groan.
As a random thought, because the polyurethane is sprayed into the panel could it have shrinkage issues and be separating from the facing in spots? Sort of a "foam checking". I know that sometimes an improper mix can cause it to happen in stud framed spray foamed installations.
Any other details or clues would be helpful...