Big props to Ubuntu for taking a risk and trying to innovate in the desktop experience arena. Unity is pretty cool, but pretty raw, too. For example, some apps don't yet support the new panel. Even worse, some apps can get stuck in a "headless" mode where you can't access any of their windows due to not having a panel icon.
Here is how to fix that. For a specific app, just add it to the whitelist. Hopefully these apps will be updated soon, making this a temporary fix.
>gsettings get com.canonical.Unity.Panel systray-whitelist ['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray', 'scp-dbus-service'] # added keepassx >gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray', 'scp-dbus-service', 'keepassx']"