Is it set by WinSCP or by the server to which we are connected?
I am having an issue, where WinSCP will disconnect after 30 to 35 minutes regardless of any activity that just occured. At 29 minutes I changed to a new directory and a couple minutes later it still disconnected. Also, it will even disconnect in the middle of a file transfer. I was in the middle of also transferring file during the above times and it still disconnected.
This is reproduceable every time I use WinSCP v4.2.8 on Win XP Pro sp3.
Even if keepalives are set to either Sending NULL SSH packets or Executing Dummy Protocol Commands, it will still disconnect after 30-35 minutes.