With RPVST enabled, try running show spantree instead.
This may not be much help with your current setup, but the ideal one if you were rebuilding the upstream infrastructure would be a cross-stack port-channel (multichasis etherchannel, whatever else people call it). Anytime that I have deployed a controller with upstream devices in the same segment, I always use LACP port-channels with short timers. You can avoid a lot of the spanning-tree headaches and you also gain load balancing so both links are actively forwarding traffic.
I'm very interested to hear what others have done with standalone upstream switches and spanning-tree.