I am having this same problem with the plugin that this user mentioned in this other thread: http://wordpress.org/support/topic/link-not-working-properly-1?replies=5#post-4986821
The behavior is that the file path has the characters "/download" in place of the actual file path for the upload. This will lead to a broken link unless I perform a workaround.
Example: When this is entered into the post editor..
..this sets the href property to
Please advise, thanks!