Sound like your FTP is disconnecting then reconnecting during the upload. I have had this happen with other programs. There should be a setting in the program about timeouts and resume uploads. Usually they would be int the server settings. I would provide a screen shot but  unfortunately they took my ftp ability away from me here at work.
As for using Windows explorer or any browser for that matter I have found they are better for downloading and not uploading specially large files. Another thing that it might be that the host you are trying to upload to only allows uploads to a certain size.

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