I am recalculating Averages for my large school and the process times out every time after running almost exactly the same amount of time; five minutes. I have also experienced this while running other processes.
In your SchoolLogic Virtual Directory on your web server, open the web.config file in a text editor such as Notepad. Search (CTRL + F) for "300" without the quotation marks. Here is the line you are looking for:
<httpRuntime maxRequestLength="30000" executionTimeout="300"></httpRuntime>
The 300 indicates 300 seconds, which is five minutes. Make that number larger. Note: Any changes to the web.config will restart the application and everyone will have to log back into SchoolLogic, as if they had timed out of the session -- so it would be best if you edited the web.config file when no operators are in SchoolLogic.
There is a series of steps for increasing Time-Outs for TeacherLogic which can be adapted to SchoolLogic as well. Click Here to learn steps you can take in IIS. Toward the bottom of the document, there is a section on increasing the maximum requesting entity body limit. That can also be adapted to SchoolLogic, although it is rarely necessary.