I can confirm that clearing the current binding, until it is blank, then re-assigning the keybinding will make it persist after logout / login. On first "clear" for any key-action combo affected by this bug, it actually restores the default / previous binding. On any key-action combo that *does not* have this issue, pressing clear seems to actually clear the binding.
I'll hazard a guess that the window manager was using whatever key combo appears after you press "clear" the first time.
I can confirm that clearing the current binding, until it is blank, then re-assigning the keybinding will make it persist after logout / login. On first "clear" for any key-action combo affected by this bug, it actually restores the default / previous binding. On any key-action combo that *does not* have this issue, pressing clear seems to actually clear the binding.
I'll hazard a guess that the window manager was using whatever key combo appears after you press "clear" the first time.