Hi,
if possible, please post here a link to your website so I could check it.
At first please verify that you have assigned your custom menu to the “Main Menu” location in “Appearance > Menus” (under the “Manage Locations” tab). If this does not help, please try to deactivate all your installed plugins (one after another) as there might be a plugin conflict that causes this issue.
Best regards,
Tomas Toman