I currently have my PS2 connected to this system with a NexxTech brand optical cable, I had been using a Philips optical cable, but I thought it might have been the source of my cracking, it wasn't.
Every once in a while (Seems to be happening more now) the HT will make a cracking sound, that seems to be coming from the front speakers and is only at high frequencies. It is most apparent when playing the little 'ding' sounds that accompany most video game menus.