Cisco Switching/Routing :: 6509 - VSS Implementation

I have a network with four 6509s in a ring with 10Gb links. Two adjacent switches are at the home office, the other two at the DR site. The switches at each location are physically similar to each other with respect to what blades are in them. We went through an upgrade from SUP-720's to VS-SUP-720's recently, only at the DR site - basically a practice, with the home office conversion hopefully taking place next weekend.
 
We initially just brought up the two chassis separately, in non-VSS formation (stand-alone). So far, so good - everything was connected, all traffic was passiing, all links were up, everything was reachable: EVERYTHING worked. Then we made the conversion: step-by-step from the cisco.com page; create a virtual domain, make one switch switch 1, the other switch 2, create differently numbered port-channels on each 6509, add the SUP 10Gb links to the port-channel, do the conversion.
 
Here's where the trouble started. First of all, the two 10Gb links back to home office created a spanning-tree loop and we had to shut down one of the links. (Is there something that needs to be configured on those links to turn spanning tree on? Does VSS conversion turn stp off?) Secondly, though it worked while in stand-alone mode, the copper blade in the standby 6509 stopped passing traffic - it would take config, the links would come up, but you could not ping across those links. Interestingly enough, there was an access switch with links to each of the copper blades, and having them both up also caused a spanning-tree loop. adding a new port-channel and putting both links in it did nothing to alleviate the loop. This leads me to believe that stp is not working properly. I reiterate, that even though the loop occurred, nothing else plugged into that blade was pingable.