Project hierarchies with installation projects cannot be updated right away because the new products might not exist until the hierarchy is partially built. (If the products are in a non-writable state before the build, new versions are checked out. The new versions need to be selected into the installation project after the build is complete.) Portions of the hierarchy are updated and built in phases.
To prevent selecting new tasks, clear auto-refresh on the project grouping after the first update. Then, set auto-refresh again on the project grouping after the last update.