Do you know how long of a time period we are talking about before the user was logged out? Have you had this happen to yourself? If the problem is not one that everyone experiences the same it will be much more difficult to determine the cause and the solution.
Generally speaking the user should remain logged in while the session is intact, if the session is destroyed or deleted then you would experience something like this. The session should be controlled by the PHP server, so if this a problem on the server others should be experiencing the problem the same. If the user has some settings in their browser or security software that is killing off the session it would need to be dealt with on the client end. Please post back with any more info that you have about the problem and we will check it out to see if there is something we can do to help.