Let's start with the issue...
For many programs the notification will pop up to tell me a program isn't responding (one in particular but that will be dealt with in another issue as this is a more global system issue). However, most of the time the software will complete its task either immediately, or immediately after pressing the 'wait' button. If not, I may have to hit wait let it load a bit, then the warning will instantly pop-up again (repeat a couple times depending on if you pause a moment before clicking wait).
Is Timeout the function that controls that feature? Because I would very much like to reduce the rate of pop-ups. If not how may I resolve this?
Extending whatever response time check should make a much smoother experience (as it seems to pop up within a second of taking an action).
Also, I have noticed depending on how fast I press wait, it may close the program. Or similarly when the screen goes black (idle screensaver) it will generally exit the programs I have open. Would those be the same parameter or a different one that I may adjust?