I ran into the same issue with image upload issues that other had. Windows 8.1 and empty files were being uploaded. I solved the problem by publishing to my hard drive and then using Fling File Transfer to upload to my server every time a file is changed in my local directory. So far so good and the program is on sale for $20
http://rathdrumweather.us/radar.php
Dennis
Smart thinking, I was doing something very similar.
For future readers of this topic who haven't purchased Fling FTP, I've written a free version that is aimed at GR3 web publishing.
Derek