I don't currently have the St. Anne's organ installed, so I googled for an image of the console. There appear to be two Swell pedals, but only one one set of stops I would expect to be controlled by a swell pedal (“under expression”) - those on the Swell manual. I think you may have inadvertently “auto-detected” the wrong pedal. Right click each pedal and read the resulting message carefully – I would guess that the one on the left is the true Swell pedal, whereas that on the right is a General Crescendo pedal for the whole organ.
The Great to Pedal lever will only duplicate on the pedals the stops you have already drawn on the Great manual. Try “pulling out” one stop on the Great, then apply the Great to Pedal coupler, and see if the manual stop now also sounds on the pedals. Quite likely the Great to Pedal will be reversible - successive operations will turn the control on, off, on etc.