Does that mean it is the only file on the remote server? Or, it's the only file of 0kb size?
I would not rule out a server-side problem. Are the two servers hosted by the same company? Can you check the type of ftp servers they use (the unix command-line interface "ftp" is useful for this).
I can't think of any reason why the presence (or absence) of a file on the server would make any difference as far as weewx is concerned. It is ignorant of the contents on the server and simply uploads anything that has changed.
Try setting debug=2 in weewx.conf. It will create voluminous logging, but it will also give more detail about what's happening.