>I use FileZilla to upload our setup files to our website via ftp, but there are lots of problems associated with that program. For one, when the upload gets interrupted, you have to start all over. That can be extremely annoying when you have waited for almost one hour and when the upload is 95% finished it stops and you have to start all over.
>Does anybody know a good ftp program that could do the job better?

FileZilla is perfect for FTP - no problems at all that I have ever encountered. You need to set the options to "resume" or "ask for action" if the file (or part of it) already exists. It will then simply continue from where it left off. Edit menu-> Settings -> File transfer section -> Action to perform if file exists on upload and download. Yours is probably set to overwrite.