After more testing, I noticed that the description isn't correct, but the bug is on a different level. It is not about file extensions.
The local version of the directory I was working on (inside /private/var) hadn't followed a rename on the server: I had renamed 'contents' to 'Contents', and Cyberduck stopped receiving notifications about local file changes.
So, the bug is: case change on the server side don't seem to be properly followed in the temporary local directory.
I just tried the history log to see what happens. The result is the screenshot cyberduck2(access denied 530 error message). The second screenshot is ( I hope) the log you requested.
When I tried the history log try the last day I was able to successfully log in was 11/21/2014. Hope this helps.