Overlapping icons in Applications Folder Dock icon

I recently upgraded to a MBP Retina running 10.8.3 Mountain Lion.

Deciding to re-install apps and cleanup old unused stuff, I didn't use the Migration Assistant.

I opened Finder and dragged the Applications folder to the Dock. When I did so, the preference was to display as Stack. At first, it was showing the Mac App Store icon as it was the first app listed in the folder. When I installed Adium.app, Adium became the first app listed in the folder and now I have the Adium "duck" icon overlapping the blue Mac App Store icon.

If I rename Adium.app to Badium.app, the Mac App Store is the icon displayed on the Dock. If I rename Adium.app to anything alphabetically before App Store, they overlap. I've tried dragging the Applications folder off the Dock and re-adding it, running the command "killall Dock" from Terminal, logging out and back in, and even rebooting. Deleting the ~/Library/Preferences/com.apple.dock.plist doesn't fix it.

How do I get the folder to display the first app instead of overlapping or having to have the folder displayed as a "Folder"?