I've noticed that the "finish then stop" button for Folding@home doesn't work. You just have to stop a project in the middle to reboot your computer.
@AlphaCentauri
I think it means to finish the whole operation and then stop...if you need to reboot your rig hit the "pause" and it stops it immediately. It'll even allow you to pick up where you left off hours later, as long as you don't go over the time allotted for the finishing of the operation, it'll start where it stopped and continue to completion.
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@Usama_Backhair
I just hit stop early in the new project and it still picked up right where I left off. So reboot won't reduce your score from having "unfinished tasks."