Breaks never automatically wait for the next break, unless you create them by using the “Make Into” buttons.
The thing that causes problems is using the “Make Into” buttons multiple times on the same music, because, as Dan said earlier, you can’t have a Frame Break and a System Break at the same location. If you use “Make Into Frame” then the Frame Break at bar 1 is set to wait for the next Frame break. If you then use “Make Into System” then you might find that the Frame Break at bar 1 gets replaced by a System Break, or you might find that it remains a Frame Break, has “wait for next System break” set but ends up with “wait for next Frame break” unset.
Basically, the new properties aren’t added to the existing ones; they replace the existing ones.
This is why I much preferred the old solution: Frame Breaks and System Breaks (with “wait for next” properties), and no “Make Into” buttons. Under that system we users were forced to understand how the thing works! Now, it’s quite easy to use the “Make Into” buttons with signposts turned off, and not understand what’s going on behind the scenes (and why it doesn’t necessarily seem to work logically).