As a workaround, publish the site to the file system (i.e. save it locally), and then use another FTP client to transfer it. This is not great at all, but if you are desperate and out of options, this may be the solution, no matter how temporary it is.
As an actual fix, you can enable this on the server. In my case, this turned out to be a firewall problem (it provided input permissions for FileZilla Server) and did not use a custom port range on the FileZilla server (under passive)! This suggests that this is a port problem.
However, this does not explain why you may or may not disable / enable passive mode in VS 2012, but may be in earlier versions.
source share