The step to reproduce are easy and reproduceable multiple times.
Using a new install of the RnShop Quickstart....
1. I have the 'Particles' Menu setup as in Menu-1.jpg
2. In the Joomla Menu Manager, on the Main Menu, click New,
Menu Item Type > System Links > Menu Header
Title: Column Header
Parent Item: Particles
3. Go back to Gantry 5 Themes > Default Theme > Menu
Click on Particles
Menu layout is now messed up, as in Menu-2.jpg
Thanks