It's normal, its documented, etc etc
In shell (telnet/SSH):
user@machine:~/example.com$> ls -a
In CuteFTP, you need to look for "server-side filtering" setting. Well, at least that is what is called in CuteFTP Pro. Access Site Properties, then Actions tab, and there is a "Filter" button.
On this dialog at the bottom is "server-side filtering" with a checkbox and textbox. Check the checkbox and in the textbox put "-a"
If you monitor the FTP commands then you should then see your client send "LIST -a" when retrieving a directory listing.
Perl / MySQL / HTML+CSS