Project hierarchies with external 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 must be selected into the external project after the build is complete.) Portions of the hierarchy are updated and built in phases.
To prevent selecting new tasks, clear auto-update on the project grouping after the first update. Then, set auto-update in the middle of the multi-phase build on the project grouping after the last update.