It feels like Muni is under a cloud of late. One of its own making.

This week, Mission Local revealed that the agency’s new diesel-electric hybrid buses are operating without a pollution-control program that has been par for the municipal transit course since the 1980s. The buses’ onboard computers are not programmed to shut down the engine after several minutes of idling — and sources say buses are being allowed to idle excessively in the yards, a decades-long Muni malady.

Muni, it turns out, is on an emissions kick. In September of last year, it quietly agreed to a settlement with the California Air Resources Board: Muni pledged to fork over $220,500, mend its ways and make investments in training and maintenance after the state regulators alleged San Francisco’s transit agency failed, for years, to ensure its vehicles met California emissions standards — and failed to even attempt to do so.

“SFMTA failed to test, measure, record and maintain records of smoke emissions from its fleet of heavy-duty diesel vehicles for years 2013 and 2014,” states the settlement agreement. The state says some 329 buses failed to meet “the applicable in-use performance standards.”

While the Air Resources Board occasionally puts out a press release trumpeting its settlement agreements it did not do so in this case. Muni was the only municipal transit agency dinged by the state in 2016. No news stories — prior to this one — have been written about Muni’s hefty fine and settlement for evading emissions requirements.

Muni’s failure to measure, maintain and record emissions levels led, unsurprisingly, to its failure to submit mandatory annual reports detailing the above. In addition to the fine, Muni was required to remedy this and other mechanical and clerical practices. The transit agency was ordered to train its staff on emissions testing procedures — and to begin smog-testing its vehicles.

One of the settlement’s stipulations stated that “SFMTA shall instruct all employees who operate diesel-fueled vehicles to comply with the idling requirements” of section 13 in the California Code of Regulation.

The state, bluntly, is ordering Muni to cease violating the law. And, intriguingly, it was these very laws regarding over-idling buses that Muni workers allege are still being broken when coaches are allowed to rumble on indefinitely at bus yards. These are the buses, again, in which Muni opted to not install automated programs that would curtail excessive idling.

It is questionable how well this stipulation is being followed. Muni is allegedly doing one of the very things the state ordered it to not do, and its decision to not install idling auto-shutdown programs further enables that.

When queried about the settlement, Muni officials sent an e-mail claiming the situation had “less to do with the actual emissions of the vehicles than … with paperwork and regulatory policies” — and was exacerbated by the inconsistent advice and faulty equipment of the Air Resources Board.

Queries to the Air Resources Board seeking its view of Muni’s response — and asking whether Muni could be subject to further fines — have not yet been answered.