In the course of my work as well as leisure, I have used and try many FTP client softwares. Recently, I came to know that FileZilla, an open source FTP client and downloaded from http://filezilla.sourceforge.net/.
Once installed, I came to know that File Zilla is just the software that I have downloaded from www.ftp995.com except that FileZilla come without the disturbing ADs :-).
FileZilla may not have many features as CuteFTP Pro but it simply able to do the job beautifully. Uploading big web and files often end with success and little failure. Its ability to auto reconnect for a number of times which can be determined and set by you will ensure all files are uploaded.