Bug due to load order with CSS template

I bought a theme on themeforest and I am trying to integrate it into meteor.

The menus and jquery work only when I do a refresh and force the cache to be cleared.

This way the assets take more time to be loaded and the js is taken into account. Then if I do a simple refresh, all animations are dead.

What is the best practice to fix this? I suspect it is a problem of loading order, something is not ready.