There is a version of Stacks for RapidWeaver 5 and a version of RapidWeaver 6. When you download Stacks you get a disk image that contains both versions of Stacks. You should install only the version of Stacks that matches your version of RapidWeaver.
The RapidWeaver 6 version of Stacks is called:
The RapidWeaver 5 version of Stacks is called:
Note the file extensions are different.