On Ubuntu since 11.04, the taskbar is controlled by Unity, which by default does not allow all programs to place their icons there. You must configure the application whitelist so that it can access the taskbar. This is where I found the answer initially:
http://ubuntuforums.org/showthread.php?t=1737589
Basically you should call:
gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'YOUR_APPLICATION']"
, . YOUR_APPLICATION Unity.Panel. , , . , , :
gsettings get com.canonical.Unity.Panel systray-whitelist
( ) "['all']". .
, Ubuntu , AppIndicator . , wxTaskBarIcon , AppIndicator.
: http://www.webupd8.org/2013/02/unity-notification-area-systray.html