Indeed, the checkbox in the mate-window-properties window turns off by itself after I close and reopen the application. And the "Raise selected windows after an interval" option is unchecked, not greyed out.
But the focus setting itself stays turned on. It doesn't revert to click-to-focus.
My MATE is fully updated, check whether yours is the same.
I was able to partially reproduce it.
Indeed, the checkbox in the mate-window- properties window turns off by itself after I close and reopen the application. And the "Raise selected windows after an interval" option is unchecked, not greyed out.
But the focus setting itself stays turned on. It doesn't revert to click-to-focus.
My MATE is fully updated, check whether yours is the same.
Also a question: do you have compositing enabled?