It's not a bug. All template customization that you do in template configuration or by adding a variation on a position.. are saved a "style" such as other Joomla templates. Try to edit it.
When there are different parameters for different menus and indicated I can understand that you have more than one style, as in joomla. But with the same parameters for all menus and I can not understand why. The parameters of variation are in a different table and do not indicate which style applied.