That's about what I figured. Is the roof a tile (like Cepac Monier, etc), that can be accessed from the attic area?? If a guy can get in there, remove some tiles, flash like it originally should have been, maybe can solve the problem
Many sites are available online from roofing companies showing proper flashing. The problem now, with the cement block sidewalls, is getting it properly flashed where the wall meets the roof.
Hope I am understanding your problem correctly. Can you get a picture of the area in question?