A switch may see a topology change without its own designated root changing. So it's probably an edge switch of some sort - perhaps a blade or virtual switch that you haven't considered.
I would take a topology drawing of your network and mark up the switches that show these changes.. You can get dot1dStpTimeSinceTopologyChange through SNMP, to speed things up. I think it might show a path from the root to the switch where the problem is. If so I'd look carefully what "show span details" shows there.
Sorry, I'm not enough of a RSTP guru to know exactly what to expect. I've been meaning to look for my education for a while.