I can ssh to my instance and use it but if I'm not active for some time then then I must reconnect. Is it the protocol, the server or the client that causes the timeout? It happens both with cygwin and putty on Windows 8.1 (but I didn't try between 2 Ubuntu).
If you are using cygwin ssh, you can add the following to your /home/user/.ssh/config file
Host * ServerAliveInterval 30 ServerAliveCountMax 4
That should send an alive message to the server every 30 seconds and if it fails 4 times then the connection is closed.
If you are using Putty, there is a "Seconds between keepalives" setting on the Connection panel.