When you use MRP for job generation, it is highly unlikely that multi-level subassembly jobs will be scheduled to start on the same day.  This phenomenon typically only occurs when manual planning is used to create job chains.  Start date overlap is just one of many problems caused by job chaining and is best corrected by using MRP.  

If it so happens that multi-level jobs do get scheduled to start on the same day, never release the jobs all at once, which can only be done by ignoring the material shortage warning.  If you release jobs without material, they all get listed in work center queues as active jobs and there is no way to know which job sequence should be run next.    

If you release jobs only when material is fully allocated, jobs will get released in perfect order.