I was on an original ftp site, in a folder called /missionbeach, where everything worked fine.
I then used the Bookmarks button to change to a different ftp site. This authenticated and tried to open, but then gave me an error alert, complaining that /missionbeach was not a valid folder name on the new site.
After I accepted the error alert, then the proper ftp site opened uneventfully, at its root level as it should.
I haven't seen this before, often enough switching ftp sites this way, so probably you have a regression here.
Other things have cleaned up without being listed, so I think you are on a good path for another release version here. I enjoy CyberDuck a lot, not least for its name ;)
This is actually on 4.5, just downloaded, so I noted as Nightly Build in your form here, since 4.5 hasn't made it into the dropdown.