Publishing uploads 0 byte HTML file

I have just started using Sitely and have a problem uploading the site.
After using the publish option to my hosting service, if there is an existing HTML file Sitely creates a 0 byte HTML file with no content. If I log on to the site using FileZilla and delete the 0 byte HTML files Sitely then uploads the files correctly.

If i update the site I need to delete the existing HTML files before publishing.

Any ideas why this is happening?

Steve