Sorry to revive an old topic, I had this issue myself and found out what the underlying problem is as well as how to "fix" it. I thought maybe I should send in this reply in case others face the same problem.
Here goes:
The problem as I understand it is that the FTP server first copies whatever file you transfer into a cached location and then copies from the cached location into your desired directory. All of that happens before the FileZilla transfer queue is 100% completed, often it seems like it gets stuck on 99% when actually the server is just waiting for the files to be moved from the cache to your working directory.
What you can do to solve this is to increase the timeout time of the Client. In FileZilla go to Edit > Settings > Connection > Timeout in seconds: and set this to a higher value; in my case I was trying to upload a 1.4GB file with a 20s timeout, this meant that the FTP server only had 20 seconds to move the 1.4GB from the cache to the directory I was uploading in, which wasn't enough. I increased the time to about 360 seconds to accommodate the slow cache; I haven't had a single upload issue since.
I hope this helps 
