The same here. I noticed the phenomena already with former versions of Cyberduck and Mac OS. Also here I have the impression it is related with an previous download of an huge amount of files. I attach a screenshot of the activity monitor: 100% CPU, 2GB memory for Cyberduck. This hours after the transfer was completed and all windows of Cyberduck closed.
Macbook Pro and Mac Pro, Os 10.6.6.Cyberduck 3.8.1