I too have experienced this same issue, but have not had much time to 
come up with a fix, anyone got a quick fix for it?
This is on the generic pc cf/hd version.

Jesse Guardiani wrote:

>Hello,
>
>Is anyone else experiencing SSH connection timeouts
>using 1.2b3? After about 2 hours I lose my sessions.
>It isn't clean either. It's similar to what happens
>when a network connection just goes down. The session
>stays open, but if you press keys then it times out
>after a few minutes.
>
>I have nothing in m0n0wall -> Advanced -> TCP Idle Timeout.
>So it *should* default to 2.5 hours. However, my ipv4
>tcp keepalive on the machine that keeps losing connections
>is currently this:
>
>% cat /proc/sys/net/ipv4/tcp_keepalive_time
>7200
>
>(two hours)
>
>So I'm not sure why my connections are dying. This is
>a Soekris 4801-50 m0n0wall platform. Any ideas?
>
>  
>

-- 
Eric Collins
Sr Network Administrator
Tawifi.com

Downtown Tucson WiFi Network
http://www.tawifi.com