Why do some apps not show up on the dock in Mountain Lion? I'm not sure if this was intentional, or if this is a problem, but when I open the App Store or Messages, they don't show up at all in the dock, but they run just fine otherwise. Why is this and how can I change this behavior?
Here are some steps to fix problems with the Dock:


Run killall Dock from a terminal
Log out and back in
Reboot the machine
Reinstall the apps affected 
Try to create a new user profile