OAKLAND — The California Public Utilities Commission has joined BART in an investigation into Wednesday’s incident that led to medical treatment for 11 passengers after a westbound train inexplicably stalled and filled with smoke in the Berkeley Hills tunnel.

The CPUC initiates a probe anytime more than two people require medical transport from a transit accident, BART Operations Manager Paul Oversier told the agency’s nine-member elected board during a preliminary incident briefing on Thursday.

The scary mishap is the latest in a series of operational problems that have plagued the massive system in the past two months, including a fire on a train near Orinda in late October followed by stray sheet metal on the track in the Transbay Tube and a software upgrade gone bad that shut down the system for hours in November.

“I feel that we, as a board, need to do something about this,” Director Zakhary Mallett said. “The public has been through a lot. Our brand has been severely affected.”

The Wednesday accident began with what Oversier described as a rare malfunction that spiraled into a major incident.

“I was listening (to the radio communications), and it was as bad I’ve ever heard,” Oversier said.

About 8:20 a.m., a nine-car San Francisco-bound train ground to a halt at six-tenths of a mile inside the Berkeley Hills tunnel. In train parlance, it’s called an “irretrievable stop.”

The operator — a part-time employee who had been on the job 1 year and 9 days — ran through the standard troubleshooting procedures and communicated via radio to the central dispatch center, whose computers indicated the problem was an engaged parking brake and an open door.

She was also getting passenger reports of smoke and a bad smell.

Each BART car has two types of operational brakes in addition to a parking brake. The dynamic braking system ensures that equal force is applied on each of the two rails, but if those two forces get out of sync, the computer throws on the friction brake.

When that happens, the wheels or trucks on the car heat up and generate a burning odor and light gray smoke. And because of an unfortunate design on the 40-year-old cars, the smoke and smell are sucked into the cars through the air-intake grill located near the brakes.

Per protocol, the operator started going through the packed cars one by one and checking the brakes. In the eighth car, she found what she thought was the problem, fixed it and made her way back to the cab, Oversier said.

But the computer still showed she had an engaged parking brake. She went back down the line and, sure enough, in the ninth car, the panel showed all three brakes were engaged.

“She (releases) the friction brakes and the dynamic brakes, but she does not cut the parking brake,” Oversier said.

The train still wouldn’t move, and, 23 minutes into the incident, passengers were having trouble breathing. For safety reasons, the operator could not open the doors, so she rolled down her cab windows and let people into her tiny cab.

Things went from bad to worse, Oversier said.

BART turned on the tunnel ventilation fans, but the computerized doors on the Orinda side of the tunnel wouldn’t open, blocking not only air flow but a rescue train from the much-closer Orinda station.

Finally, 49 minutes after the “irretrievable stop,” BART sent in a rescue train from Rockridge. A technician fixed the problem, and BART crews moved the train holding the stranded commuters through the tunnel.

It’s unclear why the parking brake improperly engaged or why the locking system on the tunnel doors jammed.

BART has put out a bulletin to all train operators about where to find and disengage the parking brake — because it rarely malfunctions, train operators don’t have experience releasing it, he said.

In addition, BART will meet with the fire departments for a post-incident discussion about improving their coordination.

The final investigation report and its corrective recommendations will be made public when completed and submitted to the CPUC, BART staff said.

Contact Lisa Vorderbrueggen at 925-945-4773. Follow her at Twitter.com/lvorderbrueggen.