Hi Brian.
When Stanford Wilbur 7.x-2.x (or Open Framework 2.06) is used for content editing, the "Generate Automatic URL Alias" checkbox used with Pathauto on a content edit page is enabling Custom URL Alias text field, which is the opposite of the normal behavior. I have confirmed switching to Seven for content editing makes this behavior return to normal.
I suppose there must be some sort of Javascript conflict, although note this problem has been reported on drupal.org: http://drupal.org/node/1728528
There is currently no known fix, but I'm hoping the discovery it's tied to a particular theme gives people enough of a push in the right direction.
Anyway, do you think you could research why this is happening and/or provide permission to share Wilbur with the module developer so they can debug?
Thanks and regards,
Dan @webdrips