I use SourceGear's Dragnet product for tracking issues and the one thing that's always bothered me is the timeout. So I would modify the timeout in the Web.Config file as well as the IIS but it still never seemed to take it.
Much like Rick Schummer's post about reading magazines for the right tips, subscribing to the SourceGear forums is also a helpful place.
I've linked to the topic but for those who don't want to click, the answer is in the IIS setting "shutdown worker processes after being idle..."
As per users gmagana and kbonnin, In the IIS 6 Admin: Application Pools -> Properties -> Performance -> Shutdown worker processes after being idle for (time in minutes).
So I created a new pool just for the Dragnet app and set it to 720 minutes which should be sufficient so it won't time out.
What's sad is that the original report on this was made in April 2005 and then updated again in September and I've been living with it for months now. Hopefully this post will make it easier for others to find it.
support.sourcegear.com :: View topic - The assault of the Error 500's