Drupal not loading Civi's CSS and jQuery
Check what caching you have set up in Drupal. My suspicion is that aggressive caching somewhere is taking a snapshot of the head on a non-Civi page (since that's most of your site) and presuming that it's the universal header.

You might try disabling all caching and see whether it continues to break an hour or two after you clear your caches. Alternatively, look through any cache modules or services you've got and think whether it might cause this.