Check the order of categories
Function is disabled
Function "Split categories left to right into columns" is enabled. It allows to change the direction of columns filling with subcategories in the categories popup.
How to enable function in the Magento admin
This is a step-by-step guide on how to specify Responsive Custom Menu Free Magento Extension settings in Magento templates.
This extension will adds an useful, professional and nice navigation menu from all active categories.