That can happen, but it's annoying. Sometimes a stack appears again and again in the update window and wants to be updated, even though you just did that. The solution is quite simple - if you know how.
Launch Rapidweaver and open the Rapidweaver/Reveal Addons Folder menu. A Finder window opens. In this window there is a folder called "Stacks". This folder contains all installed stacks. Find the stack that's bitching and move it to the desktop. Now finish Rapidweaver and double click on the stack on the desktop. It will be installed again. Afterwards it should not ask any longer for an update. If it still does, it can help to download the stack again from the stack developer and reinstall it.