If you use a decent FTP server software which supports a hash function (XCRC, XMD5, ...) the file is only uploaded if the local file is different from the remote file. Comparing the files by the file time only works reliable if the server supports MLST/MLSD and MDTM to set the file time. Another problem would be the time zone of FTP server if the file time is not based on UTC.
Most if not all FTP servers developed for Windows already support features which eliminate the problem. In comparison most FTP servers available for U*nix don't. In conclusion you will only run into the problem you mentioned if you are uploading to a FTP server with limited features (no hash function, local file time, no way to set file time) on U*nix.
We will try to find a way to enhance the current file exist logic to achieve what you are looking for.
Regards,
-Mat