Problem - SIS session times out in less than 20 minutes of inactivity, and there are two windows open when this happens.
This is not a new problem. It depends on how you opened the second window. Once logged into SIS, if you go up to the IE menu bar and do File > New Session, then you have a separate timer running for each window, which is what you want. If you use the open in new window button within SIS, or if on the IE menu bar you choose File > New Window, then both windows are still tied to the timer on the first one. If you are not active in the first window, it will kill the second one no matter what you are doing in it.
Activity means sending transactions to and from the server. Scrolling, moving the cursor, or typing data in a field are not recognized as activity.
This is a problem with other applications we have as well. The easiest way to handle it is to run two different browsers (like IE and Firefox) and to have one session open in each. They don't use the same methods to store session cookies (timers in this case), so they can never conflict with each other. They are truly separated.
If your IT folks won't give you a second browser, try the IE menu bar trick with File > New Session and see if that helps.