Okay I have a theory. Let me know if this is totally out of left field. When the stream was rewriting. It would rewrite files that had a URL in them matching http:// this would make the files have different file sizes in transit and would cause a file size check somewhere to fail.
Now that it is switched to look for only http://learning.usuhs.mil it does not find that URL in the file and therefore does not rewrite it.
I was able to verify that it would rewrite .txt files and I think anything that was not sent as a binary stream. That's what makes me think this is possible.
Does this sound plausible or does anyone have a different theory?