The transfer probably got interrupted. Use the queue (instead of direct mode) for all transfers for automated resume.
I am having a similar problems. I have many clients that must FTP thier grant submissions. The companies have suggested only a few applications for this and your s was one of them. I use an older version at home and love everything about it. Yesterday I was in a remote seesion with a client, and showed her how to upload a PDF file which transfered succesfully. After about 20 minutes she called back saying her file was not able to be opened. I looked at the file and it was only 1 Kb.
At the same time I had shown a coworker how smartFTP works. I had her upload some files to our FTP site. After the client had problems, we restored it with shadow copies. However, I was curious if it was specific to her session. I checked the files my coworker uploaded, and they were not complete on either side.
I tried to recreate the problem and it happened on my PC as well. I will try again soon as I would like to share the log files, so you can see them. It has been succesful when I put the file in a folder or a zipped folder. Is this required when uploading with the newest version. I have found some similar problems while searching the forums. I will post the logs when I have a spare second to recreate the problems. I will try to get some screencaps as well.
In the meantime I have suggested clients at that particular site use something else, however I have always liked you program and would like to suggest it again.