You don't mention changing your FTP passwords after finding and removing the virus.
Also, what FTP program are you using? Many of the free FTP programs like FileZilla and CuteFTP, store their saved logins and passwords in a plain text file. This makes it easy for viruses to steal.
I recommend WS_FTP because it encrypts the stored information.
Also, check your site for backdoors. We typically see these as .php files with either the first line or last that start with this:
Code:
<?php eval(base64_decode(...
and then a long list of characters.
These backdoors allow hackers to remotely infect websites after the owner has changed the FTP password and removed their other methods of infection.
Please post back here with what you find.