Hi Martin -
First, thanks for a great program! A guy on my team and I hit this today, and tried some extremes like re-installing, etc. Running the current version 6.1.2. This somehow was effected by performance, including network. He was able to connect to any directory on the server except for one, which has a very large number of folders in it (8027). It does take some time to enumerate (the server is linux and its drive is slow), and he was seeing this error reliably.
He played with Edit > Advanced > Connections > Keepalives --> "Execute Dummy Protocol Commands", until he got a successful read, and somehow that cleared the problem. He had also changed the seconds to keepalive to 29 (timeout -1). Once that worked the problem was gone. I suspect some sort of bad behavior on timeout? Perhaps something not de-allocated or cleared properly?
Hope this helps