You might find it helpful to edit the interpretation rules:
Scroll down to "Edit interpretation rules for all items of a specific kind".
If you don't find anything that you can adjust, perhaps batch transcode to a format so the unexpected profile falls off. (Not sure that will work, but worth a try.)
I'm having this exact issue. I see no way of removing the "embedded" profile from any file. This is with the latest version of Adobe AE CC 2015. v 2015.3