After an update or install Stacks will do it's best to incorporate the new content into your existing design -- however sometimes updates can be very significant -- include brand new components -- or remove old ones. In these cases Stacks may not be able to display all the updated content.
The solution is very simple: Quit and Restart RapidWeaver. That's it.
This will purge the old stack content from memory and only load in the newly updated info. Then you're good to go.
If you still notice problems, then it's probably best to contact the developer of the stack directly and report the issue.