OK.  I have somewhat the same issue, but maybe the following will provide some clarity.  My Documents module contains two types of files: *.jar files and *.jad files.  All jar files can be downloaded.  All jad files cannot.  All files are in one and the same folder and have very similar names.  Folder permissions are set correctly.  The potential for a mistake on my part here is minimal.

So, it looks like my issue is a known IIS 6 issue, where IIS will disallow the download of unknown file types.  The question is: how come this just popped up?  It used to work before my latest upgrade of DNN.