I installed 3.5.1 today after letting Cyberduck upgrade me to 3.6.1 yesterday. With 3.6.1 I had a number of times where the file listing would simply disappear and would come back on refresh. The last straw was when I could no longer download files -- there was a message in the transfers window saying the download had failed and something about the server setting an invalid id.

These were accounts on a linux server

I'm a heavy user with several dozen saved bookmarks with different user accounts on the same servers including some with root access. I have not had serious issues with Cyberduck for a couple years. It was a big surprise to suddenly see a release version this problematic. I'm not sure what version I was using yesterday, but everything had been working perfectly for a long time.