From what I can tell, the way in which you implement PVST in ArubaOS 6.x is important. Here's what I'm doing. Note that the priority is set to ensure that the controller is never ever ever ever ever the root.
spanning-tree mode rapid-pvst
spanning-tree vlan x
spanning-tree vlan x priority 65535
spanning-tree vlan y
spanning-tree vlan y priority 65535
spanning-tree vlan z
spanning-tree vlan z priority 65535
....
Give that a try and see if that is successful. I'm assuming you lost connectivity having two (redundant) links to your controller. You can try disabling one of the links with PVST enabled on the controller and ensure connectivity persists. Use "show spanning-tree interface <interface>" on the controller and your upstream switches to ensure it has converged correctly (i.e., for each vlan, you should definitively see one of the ports in a blocking state within each vlan's topology).