Since WA moved to "stateless" in version 6.0+ you should no longer have to contend with any timeout issues. You may want to have a look at the propertysheet for the WebAccess virtual directory. First ensure its running as an Application, then Click the Configuration button, App Settings Tab - should take you to the right place.
Before I have you go and make some modifications that may not provide an immediate result - maybe you can try a better explain what is acutually going on here...
From the sounds of it something may definitely not be configured right within IIS since from what I understand terminated sessions are no longer the case with Abe Workflow Server 6.0+. Personally I have left mine logged in for over 24 hrs, only to come back the next day and use it w\o issue.
I would do a bit of research with Microsoft on controlling the session state of applications and see what they say.
I must admit I'm a little out of my league here. I'm by no means an IIS expert or a Windows server administration guru. I don't even know what session states are! I do know that the way our system is currently set up, it does time out after a certain period of time (don't know what that is on our production server, but on our test server it is 20 min.). I have had users complain that they want this time limit extended or removed, so I'm trying to remove it if possible.
The default is currently set to 20min - I ran a quick test here and if you de-Select "Enable Session State" chkBox you will be unable to login.
I was under the impression that WA no longer relies on sessions, more of a stateless connection. Meaning that everytime an action is performed in WA by an EU it looks in memory ( I think ) for past credentials for that person and uses it again to reconnect. This allows the abilty for web farming.
InTempo (older version) relied heavily on ASP Sessions which was indirectly related to the setting in IIS.
You may wish to ask your IIS Admin or possibly bring it up with Adobe Support. I'll see if I can follow-up with a bit more research but I'm quite busy at the moment so it probably won't be until late next week.