If your BART ride seems extra crowded lately, there’s a reason: BART cars are mysteriously being knocked out of service while traveling through the Transbay Tube, forcing the agency to run shorter trains.

Thousands fewer spaces than normal are available for commuters because of the problem, which BART has been unable to pinpoint since it popped up last month.

BART has 80 cars in the shop with burned-out electrical components on their propulsion systems. The problem has mushroomed this week — on Monday alone, BART lost 40 cars to the tube gremlin.

“We do have a problem,” BART spokesman Jim Allison said Thursday. “We determined where it is occurring, but we have yet to determine why it is happening.”

The “where” is somewhere in the eastbound direction of the tube. Allison said the problem first appeared on a handful of cars starting Feb. 20 and has gotten worse in recent days.

One source inside BART told us that officials suspect that the cars are being damaged by some sort of power surge as they pass a substation near the east end of the tube.

There’s speculation that the problem might be related to work done by BART over two days in August, when crews replaced 12,000 feet of rail inside the tube and on the elevated trackway between West Oakland Station and the downtown Oakland tunnel. As part of the job, 300 third-rail insulators were cleaned to prevent arcing.

BART brass huddled Thursday trying to get a fix on the problem, said our source, who asked that his name not be used because he is not authorized to speak for the agency.

The timing is especially bad for the transit agency. Average weekday ridership in February was a record 446,660. Part of that crush was attributed to Super Bowl festivities in San Francisco, but there’s been no letup since then. On Tuesday, for example, BART reported 456,372 riders.

On Thursday, The Chronicle reported that the commute hour crush has gotten so bad that the the agency plans to roll out a BART Perks program this spring — using games, social media and cash incentives to nudge riders to off-peak trains.

With an aging fleet, BART faces challenges even on a normal day in getting the minimum of 552 cars ready for service. The mysterious propulsion problem has made that impossible: On Wednesday, BART fell 21 cars short of the bare-bones level.

“That’s definitely below our standard,” Allison said.

The result: Eighteen trains that should have had been the full 10-car length ran shorter than that. With a single car able to carry about 150 passengers, it’s been a tight squeeze all through commute hours.

Some commuters have noticed the difference, including Gene Yates of Alamo. Waiting for a train Thursday afternoon at Powell Street Station in San Francisco, Yates said, “It’s gotten thicker. It’s been packed.”

Adele Dow of San Leandro said, “I noticed it the other night. I was on a train that had a breakdown at Coliseum, and we had to wait for three trains to San Leandro because of the shorter trains.”

Allison could not immediately tell us how many other train cars with burned-out components — in addition to the 80 now sidelined — have been repaired and put back into service since the problem began.

To make matters even more confounding for BART, the problem has affected only the newest cars in the fleet — the C cars that came into service starting in the mid-1980s. All those cars have control cabs that make them versatile enough to be used on the front of a train to pull it, or to be placed in the middle.

On occasions when the Transbay Tube problem has knocked out a train’s lead car, the train typically has been able to limp to the end of the line thanks to a push from trailing cars. But the upshot is still a stop at the repair yard.

The latest troubles come as BART is preparing to ask voters in San Francisco, Alameda and Contra Costa counties in November to pay for $3.5 billion in train system improvements.

None of that money would pay for train-car replacements, but BART has lined up other funding sources to purchase a portion of its planned new fleet. Those cars are expected to arrive between 2017 and 2021.