What do you use for backups to ftp server?
I've tried the setup with Amanda and virtual tapes on the ftp server mounted with Curlftpfs and I'm not satisfied with it. I just don't feel confident about Amanda.
Also I cannot use anything that uses rsync on the ftp mounted filesystem because it only creates the directories and doesn't create files as it cannot execute "mkstemp".
I've been thinking about Bacula but I can't find any good HOWTO for it.
You could try duplicity, it can make incremental backups and send them to a FTP server, gmail, Amazon S3...
Try streaming tar or dump into ncftpput. Sometimes the simplest stuff works most reliably...
This might help... http://www.miek.nl/projects/rdup/ - used bacula sometimes myself (is ok... may not solve your issues tho).
I'm not sure FTP has the facility to allow you to properly do incremental backups. Without wanting to do the whole 'right answer, wrong question' thing, is FTP really the only protocol you can use? If it is, you can probably kludge it by doing the backup to somewhere local, looking for the changes there, then uploading them to the ftp server.
You should use the Ubuntu version of CloneZilla. It allows you to backup a image of your drive to a FTP server or a NetBios share, all from a EZ bootable disc.