Yes. You have a tough one. That's because you have two layers. But your
"outer" roof is still young.
The leak is higher than your roofer suspected; I know that because he didn't
fix the problem. Maybe you didn't tell him that you have two roofs.
The wet spot you see is a consequence of the OLD leak in the UNDERLYING
roof. IOW, the new roof is leaking at a higher eleveation, and the water
runs between the layers, only to percolate through the aforementioned old
leak.
Why do roofs leak? Sometimes because heavy feet damage the membrane. So
suspect the pathway commonly, and casually, used on the roof. But on a roof
so new as yours, look for outright tears and cracks. And don't forget to
inspect flashing and the caulk that may be required. Is there a chimney in
the mix, here?
If you want to fix a leak, you must "think like water."
And look beyond "hog valley." The water is running to the valley, after
entering in a place you least suspect.

"jj3000" wrote
It's been raining and that spot is wet again. I think the roof guy
will warranty his work but I might have to find a way to fix it myself
because I'm in CA and it doesn't rain very often. My roof is about 8
years old and it's got a layer of old roof below it already. It could
be leaking down from some other spot but I would think it's likely the
valley..

Any advice is appreciated.