Well, sfc did make "repairs", but it reset the themes for Logon Studio and BootSkin.
Yes, it will do that. You should simply be able to reapply them after.
It also broke the Windows theme engine.
Not sure what this means. Did you have some sort of theming patch applied, like VistaGlazz or something?
Which version of Fences am I running now? Well, the installer now ran, but it won't take affect. Somewhere, it stopped the install after requesting a reboot.
Try verifying the install through Impulse.