I have done a bit more research on this subject, and here is some of what I have found-

These are notes from CoreFTP's Help Manuals:

Site Settings - SSH

Simulate ASCII mode for SFTP -- Applies to "Putty compatible" mode only which does not support ASCII mode by default. Check this option to add a CR to each LF when transferring text files.

</help snippets>

This is very interesting- it seems as though this would be the responsibility of the client (me :) ) to adjust these.  I am going to read more about encoding, etc.  I believe this is starting to explain what is going on.

Thank you