Every once in awhile I have trouble connecting with the ftp client using the username@whatever.com - if you are the only one connecting to the site, you can just have your connection setting switch to your subdomain folder upon connection.

I suggest that you name your connections different within your client so you can tell the difference between when you are connecting to your main site or your subdomain.

Not exactly the answer you were looking for but something that might work in the meantime.