Any update on this? I am encountering the same issue.
Hey
So this is what my business IT infrastructure Engineer said to me...
Microsoft themselves have disabled the custom script feature on a SharePoint as a standard feature. ( he confirmed this with Microsoft). It can however be enabled for a specific site (your IT admin can do this if not you) but it will auto turn off after 24 hours.
Due to how long it take for my business to push through updates i get about 48 hours sometimes 72 before it resets.
Uploading the files itself they need to be converted to the ASPX file I also find that in the Story content folder and the Mobile folder once you have uploaded them to SharePoint you need to create the blank folders "notes" and "slides" in each as SharePoint wont upload these empty folders
Hope it helps
