I think everybody likes to go do other stuff while the computer is thinking through stuff. I don't know if its ClipWrap 5.8.2 or if its Mac OS 10.8.2 but all my processing seems to go on pause while my computer is idle.

Hi there - first off, you should be sure you're running 2.5.8 if you're on 10.8.2. You can get a fresh copy from:
http://www.divergentmedia.com/filedownload/clipwrap

That said, it sounds like your computer is actually going to sleep, which will suspend all activities. You can check that in the "energy saver" section of your system preferences.

-Colin