I am looking through the dual spec stuff again. In general, the dual spec features work, just not in ways that are immediately expected and are cause for confusion.
The dual-spec option on the bars does have a possible bug, but once you re-log the bug should vanish. But like I said, I am working through the "feel" of the dual spec features in Macaroon. Unlike other bar addons, I have to manage dual spec data on buttons where others get it handled by Blizzard server-side. So I have to go through the pains of seeing what works and what doesn't