When a user creates a theme with configurable settings the settings won't be saved for a Layout with that theme on some circumstances.
Let's see this theme descriptor file:
If the user applies this theme on Guest site's public pages and check test-setting checkbox, after saving it we will experience some strange behavior.
When the user select a child page on Manage Page dialog and select the Look and Feel section he can change the them to be applied this page directly. Note, that the test-setting checkbox will be checked. If the user unchecks it then saves the settings, after the reload of the dialog the checkbox will be checked again.
The cause of this situation is that the typeSettings propagation to the database is depends on the default value of the theme and selected value. If these values are different, then it will be saved for the page, otherwise it won't be saved.