This might be quite late for a reply. But I have recently experienced the same issue as the server session times out prematurely.
I think I have solved this by adding this piece of code to the top of all the Admin PHP pages.
$time_set = 2*60*60; // 2hrs
This give a 2 hour session before it times out and renews on any activity!
I hope this helps even though it is waaaayyy late!