ChunkyReader is hands down my favorite comic reader for iPad. But it doesn't play well with vsftpd out of the box. The app uses libssh for ftp connections. This library uses the Extended Passive file transfer mode, which doesn't appear to be implemented in vsftpd as of yet. I've confirmed this on version 3.0.3. The app will authenticate to the server and then send the EPSV command, after which the connection just hangs until a timeout occurs. Since version 2, vsftpd has a cmds_denied parameter. So I blocked extended modes in my configuration:
This causes vsftpd to respond with a "550 Permission denied" message to the app. The app then tries the regular PASV mode and the connection succeeds!