I live near the lower creek between El Camino and 101. It always flows there, and today was no different.
Across and upstream of El Camino, Hale Creek joins Permanente (very near McKelvey Park, one of the planned detention basins). Hale Creek was flowing, Permanente wasn't, so Hale is where Lower Permanente gets its water.
I tracked Permanente up to Cuesta Drive, viewing it completely dry in several places. The creek came out from Miramonte where it's underground for a short distance, and there was a small trickle, so that trickle must seep in/dry out before getting far downstream. Further upstream at Covington, still dry.
Back on Miramonte upstream of Eastwood, you can see (if you climb a tree) the cement channel where the diversion to Stevens Creek splits off. This channel had muck in it, but was basically dry. Still dry at Heritage Oaks Park.
I finally got to where the creek crosses underneath Fremont, and there was flowing water again, although not very much. I didn't go further from there, but yesterday I saw a lot of water flowing at Rancho San Antonio Park. I think we can assume that flows gradually peter out from Rancho going downstream to the Fremont bridge.
So nothing too strange today, but no explanation as to why water would just start flowing in the middle of summer as people have observed.