To start your adventures in FTP you'll first have to open your FTP client. The top-most section displays all the commands that CuteFTP sends to the server. The right-most window displays what is on your server. When you FTP into your server you will see some directories. Both of these problem occur because of basically the same problem.
Some operating systems discern a difference between text and binary files.
But Windows machines can not have gaps. The simplest workaround is to simply delete the file off of the server before uploading a new copy.