I created a new S3 account and did a couple of test uploads and download with Cyberduck 3.2.1. It worked as expected.

Later, I uploaded a few folders and subfolders worth of data, maybe 1GB worth, to the account on Windows with CloudBerry Explorer. That worked and the listing on Cloudberry was as expected.

Then, I opened Cyberduck to upload data from the Mac. That's where the surprises begin. My bucket and it's contained directories are present. But when I try to open those directories, I get errors in the form of a Failures dialog:

Failures

The last action could not be completed due to the following errors:
S3 Error:
<s3 pathname displayed>
Request Error.. Not Found.

The transcript reads, in one particular case:

x-amz-request-id: 82...<rest of id removed for security>[\r][\n]
x-amz-id-2: eQV<rest of id removed for security>[\r][\n]
Content-Type: application/xml[\r][\n]
Transfer-Encoding: chunked[\r][\n]
Date: Sun, 27 Sep 2009 19:05:00 GMT[\r][\n]
Server: AmazonS3[\r][\n]
[\r][\n]

If I then use CloudBerry on Windows or S3Hub on the Mac, I'm able to view the bucket and its contents as expected. Restarting Cyberduck doesn't change anything.