In order for Mega navigation menus to be active, each 2nd-tier item must have at least one 3rd tier item nested below it.
In the example image below, while 'Bikes' and 'Accessories' both have 3rd-tier items nested below, the 2nd-tier item 'Clothing' is missing the minimal nested item to activate the mega-nav:
What is often the case with missing mega-navs is an added or removed item from the menu that results in a 2nd-tier item missing a 3rd-tier item. In the above screenshot, one nested item would need to be added to the Clothing tier to activate a mega-nav.