We've recently taken to FitNesse to drive our acceptance tests.
One of the frustrations we had with it was getting it to run as a service. I found a neat article on the fitnesse site that described how to do this.
We ran across a situation that was absolutely maddening, involving running FitNesse as a service. Everything worked wonderfully, until you logged off the machine. At that point, the service would die.
A fair amount of googling led me to this article at Sun, which seems to suggest that this is actually an issue with the Java VM.
The fix is easy enough... Pass the -Xrs switch in the AppParameters area for srvany (the last step before 'roll the drums' in the linked instructions).