Have you tried logging into the guest session to see how the panels react there?
A few links related to your problem:
https://ubuntu-mate.community/t/panel-not-showing-up-after-boot/7429
https://ubuntu-mate.community/t/restore-saved-panel-layout/8122
https://ubuntu-mate.community/t/after-upgrade-to-17-04-i-cannot-modify-panels/12995
https://ubuntu-mate.community/t/restore-mate-tweak-default-panel-layouts/3718