Hmm... buddy! Let me tell you something... don´t believe only in the show run, always check every parameter involved using other show commands...
Why do I say that?! Last weekend, during a new WS-3750 installation for user access, I faced a little problem... Two core´s, and my new access switch, with links to both Core Switches. Trunk was limitted only to the management vlan to avoid any problems during the intervation.
In order to avoid any other problems, I´ve increased to Spanning-Tree cost to 25 in both uplinks (1Gbps) from the access switch to the cores.
So far so good! Installation done with the first core, ok, let´s connect the second! Hmmm... lost access, let me try again, ok, accessing normal, so what happened?! Root Port from Core 1 changed to the Access Switch?! Why?!
That´s when I´ve found that one of the Core Switches had spanning-tree costs of 3004, 3019... WTH! Quick show conf (yes, it is CatOS), the Core was configured with UpLinkFast...
No biggie, changed spanning-tree cost, path went back to normal, and everything else was good! Customer will check how and when to remove the UpLinkFast configuration.
If at any time, I´ve checked the spanning-tree with show commands (not the show conf), I would see that, but... living and learning, right?!
Now I do know why some guys don´t like to do a show run, they preffer to check with other commands, I think they´re right... ;)