6e5f39a created the issue

Seriously, I have no idea why S3 does this, it's really crap.
S3 file paths don't start with a slash - but if you upload a file (not via Cyberduck) to a path that starts with '/' then it creates a folder called '/' and puts the file in there. I did this using Python/Boto.

Cyberduck doesn't show this folder - that's the bug. I know it's dumb, and I feel your pain, but I thought I'd deleted a ton of important data earlier today thanks to this S3 weirdness, and I had to login to AWS S3 web console to find the files, as Cyberduck didn't show them.

Urgh.

Thanks for Cyberduck though - love it.