Having issues visualizing this topology in my head...
Two things here. While I would recommend RVPST+ be used in any network over PVST+ I would agree the merits aren't there unless we fix the current issue.
On the switches you're going to have to have a look at their view of the topology, then cross that to what it should be. Who should be root, what ports should be blocking, etc. sh spanning-tree xxxx.
Make sure to look over the spanning tree config on all switches, or post the relevant parts here for others to look at. I've seen people do silly things like disable STP for one VLAN that could cause this.