I've been a long-time user of FTP Voyager, well before SW bought up RhinoSoft. I even paid for it too, back in those days. However, lately I upgraded to the new version, and found out that hey! It's free now! Cool!
However, all was not sunshine and roses. I too have run into the FTP Voyager Scheduler empty folder bug, wherein you perform a "Move Down" command against an empty folder and it simply sits there. In my case, it performs KEEP ALIVE tasks to hold the connection open. Critically, because this task is still executing, it will not execute any of the other scheduled tasks. See below for a log output.
[03] Fri 05Dec14 14:15:49 - Getting "real path" name to keep connection alive (KEEP ALIVE)
[07] Fri 05Dec14 14:15:49 - SSH_FXP_REALPATH: translating path: .
[08] Fri 05Dec14 14:15:49 - SSH_FXP_NAME: translated path: /
[03] Fri 05Dec14 14:18:49 - Getting "real path" name to keep connection alive (KEEP ALIVE)
[07] Fri 05Dec14 14:18:49 - SSH_FXP_REALPATH: translating path: .
[08] Fri 05Dec14 14:18:49 - SSH_FXP_NAME: translated path: /
I see that this is a known issue here on the forums, and that there are supposidly "bug fix requests" or something to handle it. However, I have a problem with this NOW.
I believe I found a simple work around. I chained a file upload to the destination folder first, uploading a single 1-byte file to the destination, and THEN performing the full folder move down.
This will always cause the remote folder to have something in it, and for then the task to complete successfully. I then set up my local-side automation to ignore that file, and things were working.
Not exactly elegant, but it's working for now. :-/