There are 2 plugins for the Xfce panel for systray icons: notification area, indicator plugin. The first one is the right one, the second one is very obsolete. What happened to me was that the notification area stopped showing some applications.
There is a “parasitic” process stealing icons from the notification area. Steps:
- killall indicator-application-service
- apt-get purge xfce4-indicator-plugin
- Uncheck “Indicator Application” in the “Session and Startup” settings.
- Log out, log in.