Just to clarify - you are running CF as a service, not manually, correct? IE, when you look at Start > Administreative Tools > Services, you seen the CF services listed there? When you do that, what is the login for the CF service? Is it still the default from installation (built-in service account), or have you changed it to be a user login? if you have changed it to be a user login, is that the same login as is being used by the people who are logging in to the server?
If, when you're having the problem of CF not serving up pages, will IIS still serve pages (ie, put an .HTML page out there and try to browse to it)? This will help to understand where the problem is.
What about entries in the log files at the time of the logout? What happens to CF requests that are in progress at that time? Try writing a CF task that will run for a while, start up PERFMON, start up the request to that long CF task, then do the logout and see if there are changes in PERFMON, or entries in the log files.
Just some ideas to get us more info to help you out...
reed