The question has aged a bit, so I'll take some guesses. Maybe it is something with cygwin? Maybe you could investigate what are the differences with "diff"? For that, I'd try running "find" on the cygwin machine and make a list of files:
Code:
find /home/www/html/site_name -type f -print > cygwin.files
Upload that to your hosted service.
Then on your hosted system,
Code:
find /home/www/html/site_name -type f -print > hosting.files
and there check with "diff"
Code:
diff <(sort hosting.files) <(sort cygwin.files)
That will show with a > or a < which file has an extra name. Maybe that differences will give a clue.
Edit: also maybe the -h should really be an -H instead, but I can't see that affecting the results.