I’ve found that certain windows FTP clients like cuteFTP in their default configuration have issues with directory names wiht dots in (such as ~/sites/domain.com) where the file is actaully a symlink somewhere else.
In one of my setups, I do this…
~user/sites/domain.com -> symlink to -> /var/www/domain.com
This was causing issues, to work around it, I had 2 options…..
~user/sites/domain_com -> symlink to -> /var/www/domain.com
~user/sites/domain.com/htdocs -> symlink to -> /var/www/domain.com/htdocs
Some windows software really does suck.