Have you saved your panel layout as a "named preference", and set that named preference as your preferred choice for layout? That can be done using MATEtweak.
Also, the saved panel layout is stored in
/usr/share/mate-panel/layouts
The file will be named
{assignedName}-tweak.panel
Within that file, you have the items flagged as top or bottom using lines showing
toplevel-id='top'
or
toplevel-id='bottom'
There will be a corresponding file
{assignedName}-tweak.layout
"Panels" are originally a Gnome functionality, where it is inherently limited to a single panel. So, handling of individual "applets" on the panel may be a Gnome-derivative.
However, depending on how the UbuntuMATE has evolved the code for handling the existence and definition of multiple panels, it is likely that the code for "mate-panel" is the source of the issue.
But having said all that, you can look at the very useful info and guidance provided here. Basically, copy your named preference layout file to
cp {assignedName}-tweak.layout default.layout
and that makes it permanent! 
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There is also an informative posting on the LinuxMINT forum regarding additional stuctural details and admin actions which may or may not be applicable to UbuntuMATE.