This page holds a list of common issues you may run into with MATE.
Get the icon you would want to be your custom menu bar icon. You may want to find a scalabe version of that icon for convenience.
.icons directory doesn't yet exist inside your home directory, create it. (Beware that
.icons is a hidden directory.) Then copy your custom icon into it.
Start dconf editor. Then go to
org > mate > panel > menubar.
In the right window, you see the configuration options for
menubar. Select “icon-name”. Click into the “Value” field. Then type in the name of your icon file without the file extension. Press [ENTER]. Done.
In MATE 1.6 MateConf has been replaced by GSettings/dconf. You should now use
dconf-editor and/or the command line tool
gsettings. You can find more about it in the manual for GSettings
This issues has been observed in multiple distro's so far. It has been reported on Debian (wheezy) and Arch Linux. This is currently a known issue (dd 2013-04-21).
This is a bug in gdk-pixbuf, see https://bugzilla.gnome.org/show_bug.cgi?id=686514.