Built up flat roofs are just leaks waiting to happen.

The movement has been away from them and to things like EPDM membrane as longer lived and more reliable (Firestone makes a fortune).

Does the roof have ANY pitch?

Once water finds a path through a built up roof it can be a real chore to locate the leak.
The water can run many feet from the defect in one layer before finding a defect in another layer to continue entering.

Small repairs around vents and other holes in the roof for mechanicals can be worked on, but it can be hard in many cases to determine where the actual defect is.

We got into the attic and found where the leak is comming through the roof, but like you said the action leak in the tar&gravel might be somewhere else. We put a 4x6 tar patch over there the small leak is entering, and hopeing for the best. If that doesn't get it, we are going to have to hire someone.