By defining public $scaffold;
in your controller, you tell Cake that you want to enable Scaffolding mode, which allows you to easily insert/edit/delete some records. The scaffolding mode always uses your "default" layout.
In other words, by defining the public $scaffold;
variable, you "overrule" your layout. Scaffolding mode doesn't adopt that setting. Simply remove the public $scaffold;
line to get back to your bootstrap layout.