I don't know that I ever saw the file come up in the downloading process, I think the application simple extracts anything that exists in that directory, and not off of the items you've selected.
You're right, I think the delete cash mechanism of the mod pack only deleted what it already knows about and not the entire folders contents. If files were pre-existing in that folder form some other version of the mod pack, a newer version would not clear them out.
I went in an manually deleted the folder itself, so hopefully that does it.
Thanks!