Yes!
Right as I connect, before the LIST command even goes to the server, the TYPE gets set to A.
What does this mean?
I just uploaded the file I downloaded using Cyberduck, and the line endings were preserved. I overwrote the file.
ie. i downloaded index.php with cyberduck (which locked up finder a few times) then uploaded it with yummy - and line endings stayed intact.
Here is the excerpt, if you want the entire thing, please just let me know.
...
SYST
215 Windows_NT
SITE DIRSTYLE
200 MSDOS-like directory output is off
SITE DIRSTYLE
200 MSDOS-like directory output is on
CWD /www/
250 CWD command successful.
PWD
257 "/www" is current directory.
TYPE A
200 Type set to A.
PASV
227 Entering Passive Mode (64,34,166,113,15,14).
LIST
...