I have the same thing with Eiskaltdc++ Qt. It seems that this bug affects all QT applications which minimize to tray. The workaround with "killall notification-area-applet" works, but it takes two or three times to run the command for all the icons to appear in the tray correctly.
** Also affects: eiskaltdcpp (Ubuntu) Importance: Undecided Status: New -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/767095 Title: 1 pixel icons in notification-area-applet for qt softwares (e.g. Skype) -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs