I have now noticed that CyberDuck v 4.0.2 is also omitting content and marking certain folders as inaccessible.
I have checked the underlying permissions of the files/folders affected and I can see no differences or reasons why that content should not be available. Also, the fact that 2 different versions of the client show the same symptoms against the same server, but with different content on that server is odd.
This is because the server does not properly URI encode references in the XML response. With the new WebDAV implementation in Cyberduck, we are no more strict and ignore invalid responses. Please file a bug report with the developers of Ajaxplorer.
For example the following URI is returned
https://sphardy.com/explorer/files/public/00 How To Upload Files.txt
The whitespace in the filename should be encoded with %20.