CDN Upload Path & Content Type

Using latest version of wordpress and the plugin with php 7 and Azure CDN. Two issues:

1. When uploading theme and include files to the cdn, they’re being uploaded to a file path like d:\home\site\wwwroot\… vs \wp-content\themes\… as they should based on how the urls get rewritten by w3tc. How do I get them to upload to the correct path?

2. I’ve not seen this in previous sites, but when uploading, the content type for css and js files is being set to application/octet-stream vs text/css, etc. This is then causing some issues in loading those files for the site as the browser gets confused as to what they are. How can I stop this from happening?

Any help on these would be much appreciated!