As you may have found by now, AutoCAD MEP 2012 introduced a new user interface for ducts. The goal of this was to move the interaction to the Properties Palette for adding and editing duct, similar to the changes made to pipe and conduit in prior releases.
For the most part, you will find that the settings in DuctPreferences have been moved onto the Properties Palette, making most configuration settings available everytime you add a duct, instead of having to dig into a separate set of windows.
The following series of images shows where the DuctPreferences settings in 2011 (image on left) correspond to the settings on the Properties Palette in 2012 (on the right). In a couple of cases, settings are still found in the DuctPreferences window, and some settings are now found in StyleManager.
Click on an image to enlarge.