Expired Sessions when they shouldn't

Using WebLogic 9.2.2 on Unix

We have an EAR deployed which then contains two WARs 

For various reasons we at one stage in WAR1 we need to open a new browser window
and send the user into WAR2

Opening the second window causes a new session to be created, which is what we
expect. 

The problem is that this second session will always timeout at the time
specified in the web.xml <session-timeout /> regardless of the fact the
the session is in use. The first session just works fine. So if the timeout is
five minutes and we are constantly using the session the it will be destroyed in
the middle of us using it.

Any ideas?