Before I am ridiculed, GP himself reproduced this problem before flitting off...
Have a local directory's structure mirror that of an FTP sites. Go to dual lister and navigate into some deep directory structures in both the local and FTP sites making sure that the directories are mirrored - but do not use the "Navigation Lock" feature to do this. Then and only then, turn on the Navigation Lock. In the local directory's lister, click the "up arrow" at the top right of the lister window. The FTP directory should also navigate up. However it does not and the local directory then displays that message "The two folders are not longer in syn..." etc.
It appears that the Navigation Lock only works when you navigate down and then back up. If you are already "down", then it does not come back up.
Thanks
Dave A