"Colbyt" wrote

I read the thread and looked at your pics. I would suggest a very careful
inspection of the valley area where the two roofs meet. Water could be
entering there any traveling along the felt or first layer of shingles.
The
angle gravity factored in is about right for that to happen. Valleys and
other flashings are frequent leak points when a nail over has been done.
That is the best reason to never do a nail over.

Colbyt

I agree. Especially with the wind, which could be blowing the elements back
under the eave when it leaves the valley. Chances are, that area wasn't
worked correctly on a roof-over. It's not impossible, but since the soffit
& fascia covering are installed after the original roof, it's very difficult
to get additional roof covering (2nd layer) worked correctly in that area.

To the OP: This could have been leaking for a long time, but is finally
showing up. Wood will absorb moisture to the saturation point. In the case
of a heavy rain, wood will not absorb the saturation. The sheathing may look
good from the underside, but that's usually the last to rot, the rot
generally starts on top.