Starting with Ubuntu 11.04 (Natty Narwhal), the default desktop environment is Unity. The default policy of Unity is to limit the number of applications that can put an icon in the system tray. While the program will still be accessible from the task bar if minimized through the window minimize function, the window close handler presents the option to minimize the application, making it disappear from the task bar, and no way to bring it back up. Furthermore, even if the task is accessible from the task bar, the added functionality only available in the system tray isn't available.
As a workaround, you can add SpiderOak to the system tray whitelist. To do so, from a terminal, give the following command:
gsettings get com.canonical.Unity.Panel systray-whitelist
This will give you a list of currently set keys, if any. You will need to add SpiderOak to that list of keys. If there are no keys, type:
gsettings set com.canonical.Unity.Panel systray-whitelist "['SpiderOak']"
If you have some already, add them to the list, like so:
gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray', 'scp-dbus-service', 'SpiderOak']"
After restarting Unity (by logging out, or restarting the computer) SpiderOak will then put the icon in the system tray. This has been tested on Ubuntu 11.04 and 11.10. A future release of SpiderOak will properly address this at install time. For more information on how to get other applications to work in the system tray of Unity, check out the Ubuntu Genius blog at http://ubuntugenius.wordpress.com/2011/06/25/ubuntu-11-04-fix-show-all-iconsindicators-in-unity-panels-notification-area/.