I noticed that some icons are not always displayed in the notification area at startup which was very annoying. 
After some analyzing i come to the conclusion that it is a race condition during startup of the xfce4 session.
Silly me set a very large svg as icon for the Application menu (http://cinderwick.ca/files/archlinux/artwork-official/symbol.svg). This slows down the startup of the panel considerably and the registration(?) of the icons fails sometimes.
It shouldn't happen usually, but the race is there. Output of startx in this case is:
"No systemtrayicon available"

failing systray icons where:
  seafile-applet
  blueman-applet
  qjackctl

what is interesting is that the icon of redshift-gtk did never fail.