The Windows component objects like Buttons, Checkbox, edit box, combobox, list box, etc. and Subapp don't use the Layer properties like the visibility and the Z order...
If a button is on an invisible layer, the button is still visible.
If a button is on the 2nd layer and another button is on the 1st layer, the button on the 2nd layer could be not above the button on the first layer.
Also, the Subapp don't follows the layer as expected if the layer has special X and/or Y coefficient.
This issue has maybe already been reported.