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This Sunday, Dec. 27, 2015, file photo, shows a Chipotle restaurant in Union Station in Washington.
Gene J. Puskar, The Associated Press
This Sunday, Dec. 27, 2015, file photo, shows a Chipotle restaurant in Union Station in Washington.
DENVER, CO - JANUARY 13 : Denver Post's Emilie Rusch on Monday, January 13, 2014.  (Photo By Cyrus McCrimmon/The Denver Post)

This was supposed to be the year Chipotle put its foodborne illness crisis behind it.

Company executives highly publicized new food-safety practices, gave out millions of free burritos, experimented with a rewards program and happy hours, and even added chorizo to the menu, all in an effort to woo back diners.

But customer service problems of another sort came to light instead — slow lines, messy tables and restaurants running out of food.

“I’ve estimated that maybe half of our restaurants have a guest experience that is something that could be much better,” founder Steve Ells told investors in December.

When you’ve got more than 2,200 restaurants, that’s a lot of potentially sub-par dining experiences that the struggling Denver-based fast-casual chain can scarce afford right now. Chipotle’s same-store sales were down almost 22 percent in the most recent quarter, and stocks have lost almost half their value from before the E.coli outbreaks of fall 2015.

Ells, who was named sole CEO in December following the resignation of co-CEO Monty Moran, has promised to get back to basics and focus on the customer experience moving forward.

An infusion of four new board members — including two loyal to activist investor William Ackman — will be watching closely in 2017 to see if he can make good.

Read the rest of the top business stories of 2016