Nope, doesn't sound familiar.

Are you using WF version 3 or an earlier version? If "3", are you running the current beta v3.1 or the released v3.0?

Can you enable the option "keep ftp session log" ( http://www.watchftp.com/wfhelp/ftp_server_settings_en.html ) and after running the task for some time:

Right-click the task
Select "Explore Task Directory" (the entry below it, it shows something like "C:\ProgramData\WatchFTP\MyTaskName")
Windows Explorer will open, you will see a file called 20120823.log (yyyymmdd.log).

Please zip the file and email it to me (gert /at/ gdpsoftware -dot- com) or post it here. The file doesn't contain passwords (but it does contain ftp servernames and userids).
Please also tell me the name of the file that is not downloaded

"blacklisted" happens when a file could not be downloaded for some reason.

Can you install the WF3.1 beta instead? See http://www.watchftp.com/cgi-bin/yabb2/YaBB.pl?num=1345099377
There are many changes/improvements so that may fix the issue.

If you are the owner of a WF2.x license you can find your new license for version 3 here:
http://www.gdpsoftware.com/en/customer.html