If I am not wrong, you are running a single job A every two hours and the processing time is more than two hours(my assumption). So job A starts at 9 AM and the second job ready to release at 11 AM. But the first job is not finished after 11,and as scheduled the second one is started.
You can create an event and trigger the background job.
Please check this link. It might be helpful to you.
Scheduling background job by triggering an event - ABAP Development - SCN Wiki