Jobs inside a large box with many nested boxes are not running on their own. Each job must be force started to make them run. Job dependencies within the box are not working.
This can occur if, for some reason, one of the levels of nested boxes goes to a completion status prematurely. A job within a box will not run unless the box it is in is also running. This holds true all the way to the top of the box tree. For example, if jobB is in BoxB, and BoxB is in BoxA, both BoxA and BoxB must be in a running state for jobB to run without manual intervention.
Typically, the only way to correct this type of situation is to manually run the jobs within the box tree that have not already run. If there is a box up the tree that has prematurely completed, it could be restarted. However, this may cause jobs to run again that have already run. Therefore, the best course of action is to manually work through the rest of the box flow.