f6cb038 created the issue

If you have navigated to a folder by using a bookmark and want to right click (control click) on a file to select "open Web URL" Cyberduck will forget the path to the file. It instead will assume that this file you want to open is in your root directory. (e.g. http://www.your_domain.com/the_file_you_want_to_open instead of http://www.your_domain.com/folder/folder/the_file_you_want_to_open)
The bookmarked folder and everything before it is forgotten about. I've only had this happen when using bookmarks, if I navigate to the folder manually it works fine. But bookmarks are such I time saver, it's a shame not to be able to use them.