In the Site Editor (the Connect > Edit/Add button), you can disable the remote directory listing cache from the Advanced tab. Deselect the Use default advanced settings check box and make sure the Enable Cache check box is unchecked.
If you alter the Enable Cache setting in the General Settings dialog, cache is disabled on all sites that use the default advanced settings. You can also modify the cache hours value, for example to 4, to tell 3D-FTP to reread the cache contents when it is older than 4 hours.