mate-panel is one of my least favourite parts of MATE, especially when compared to Xfce4’s panel. Its configuration is very fragile, e.g. changing screen resolution can move applets around.
Thinking about how I switched marco to i3 a while ago, it might be time to try…
Edit:
Meh, doesn’t work properly. It will run from a terminal after log in, but not during the session start, and once running logging out doesn’t work (it needs a running Xfce4 session).
Back to mate-panel… 