First of all Agile is a great theme and easy to customize, so good job to those involved!
I have 2 issues at the moment that I hope can be resolved.
1) Drop down menus are missing in chrome, I think this may be related to the # page section anchor links in these menus as was mentioned in previous topics, but apparently the fix should be in the latest package on codecanyon which I have, and still no drop-down menus in chrome. Does anyone else have the same issue or a solution for this?
2) The spinner used for the general theme/page loading animation (the colored ball). Where does one customize that?
Everything looks normal on the website. No errors and files look ok. Have you tried disabling all plugins to see if the issue goes away? I see at least a plugin called Floating Menu WordPress plugin which is supposed to work on WP navi menus as well. Not sure why you need this and may be that is the culprit. All the submenu items are populated.