Chipotle Mexican Grill is trying to stage a queso comeback, but it's proving to be a slog.

Despite worries that the fast-food chain's fortunes would be dragged into a pit of hot, drippy cheese, Chipotle managed to more than double earnings compared to the same third quarter last year. Sales in restaurants open at least a year were up 1%, another positive sign.

But that apparently wasn't enough for investors. Chipotle stock tanked after the market closed. It was down $29.30, or 9%, to $295 per share.

"There is a sense that Chipotle's rebirth is running out of steam. In our view, this is concerning given the still fragile state of the brand and the highly competitive environment within the fast food market," said Neil Saunders, managing director of GlobalData Retail.

Chipotle has been trying to claw its way back to the top of the fast-food heap ever since its E. coli scare a couple of years ago. Last month, the restaurant chain rolled out its new melted-cheese snack, queso, nationally in keeping with an industry trend — but immediately ran into protests from customers who felt it didn't measure up.

The good news? The backlash by dip devotees apparently didn't show up on the bottom line.

Chipotle reported net income of $19.6 million, compared to of $7.8 million in the third quarter of 2016.

Earnings per share were $1.33 cents on revenues of $1.13 billion, below the $1.63 on $1.14 billion Thomson Reuters I/B/E/S expected in the quarter that ended Sept. 30.

Although Chipotle appeared to be clearly on the comeback, it acknowledged it could have done better if it weren't for hurricanes Harvey and Irma. Also, the company incurred an estimated $18.2 million liability related to a data breach in March and April, when thieves used malware to steal customers' payment card data.

And it's not giving up on trying to win the hearts of queso fanatics.

The chain had said it was taking its time to perfect a version of the much-loved spicy cheese dip that was free of artificial flavors, colors and preservatives. Once queso debuted across the U.S., people turned to social media to criticize the taste.

During the third quarter, Chipotle also dealt with two food safety scandals. In July, rodent sightings forced the temporary closure of a Dallas location and a norovirus scare closed a Virginia store for two days.

More:Fast-food chains melt cheese lovers' hearts with queso

More:Chipotle closes Dallas restaurant after rodent sightings

More:Which quick-serve chains have the most loyal customers?

“Despite several unusual impacts during the quarter, including the impact of hurricanes, we maintained our focus and saw some encouraging signs," CEO Steve Ells said in a statement.

During the analyst call, Ells said the company still has work to do, including menu innovations, training efforts and "restoring customer trust."

He also reported a 51% increase in digital orders.

Follow USA TODAY reporter Zlati Meyer on Twitter: @ZlatiMeyer

