See http://community.logos.com/forums/t/91775.aspx
This isn't a bug. The command box has only ever supported Bible references, and doesn't support other references unless you specify the resource.
So you can type Open Confessions to Aug., Conf. 11.13, but you can't type Aug., Conf. 11.13 on its own.
The limitation is probably for performance reasons as much as anything.
