Just a guess but it looks to me that unless there is a hole or crack on the penthouse top, that you surely would have spotted by now, the water must be leaking in from around the roof hardware for the latches. These would need resealing.
Jage is the expert. Here is his definitive posting on the subject.
Roof Leak Repairs Round II - The Front Section
You can either repair them all or try to first find where the leak is. Someone mentioned before (can't find the thread) about using a PVC pipe standing on end large enough to fit around the outside of the hardware on the roof. Seal the bottom edge of the pipe with butyl then filling it with water. If the water goes down you know you've found one that leaks.