"I just created a new "amended file" from the original as one should"

You want to use the original file as the amended....dont try and use a "new amended file"  for the amended return.

I personally dont even make a copy of the file, I print out the original (or save it to PDF), then I keep that same file I efiled originally, mark the Amended boxes and Efile it.  Done several of these already, they all Efiled fine.