Hello Adam,
I have the same issue. I tried to use your online example to reproduce it, I found the example page doesn't work. It only shows a bunch of broken image links.
My code calls "editor.EnableStripScriptTags = false;" before loading the content which contains JavaScript from the database and set to the editor. The JavaScript code is being replaced with: <!-- Inject Script Filtered -->. I found it only happens when I set "editor.EditCompleteDocument = false;" that I need to edit content body only. When I use "editor.EditCompleteDocument = true", everything works fine. But I do need to set "editor.EditCompleteDocument = false;" and add JavaScript inside of the content. Any ideas?
Thanks.