I figured this out: Instead of using media button on the toolbar, click "Insert" from the top menu and "Choose" on the very bottom. A finder window will open, in the left pane click photos. You will see a new page open with two panes. Top pane will have expandable links: Aperture, iPhoto and Photo Booth. Click on "Aperture" and it will expand to show you your full Aperture library. Choose the project and then choose the photo.
In the old version i was able to choose media and photos from my Aperture library directly, in this new and improved version you have to make a few extra clicks.
VP