Hi Dave,
I also noticed the way you are referring these two files leads to Kentico serving non-compressed files
/CMSScripts/Custom/vendor/modernizr-2.8.3.min.js - /CMSPages/GetResource.ashx?scriptfile=/CMSScripts/Custom/vendor/modernizr-2.8.3.min.js
/CMSScripts/Custom/vendor/respond.min.js - /CMSPages/GetResource.ashx?scriptfile=/CMSScripts/Custom/vendor/respond.min.js
This will make sure that these two are also served properly.
Cheers,
Chetan