In ubuntu 13.04, after a fresh install. Unity does not show some running apps in the unity bar or when alternating app with alt+tab. when upgraded from 12.10 this did not happen.
Example apps: terminal, repository-software-manager
Temporary workaround might be to use Meta + w to get to all open apps.
That has happened to me, too. What I did about it was unpinned chrome (though, it may be a different app causing this problem for you), then pinned the terminal, and that fixed all of the other apps for some reason.