It seems that management's plan to turn Action Alerts PLUS holding Panera Bread (PNRA) around is working, but year to date the stock is down 2.7%. Why can't investors make any dough here?

Over the last two years, Panera has been rolling out its transformation plan, called Panera 2.0, to its company-owned cafés. While the plan has driven same-store sales higher, the stock has done nothing.

On Tuesday Panera reported third-quarter fiscal 2016 earnings of $1.37 per share, 3 cents better than consensus estimates. Revenue rose 2.9% to $684.2 million. Company-owned bakery-café sales increased 3.4%, while franchise-operated bakery-café sales increased just 0.2%. System-wide, same-store sales increased 1.7% among the 2,024 bakery-cafés open as of Sept. 27. At the end of the quarter, 66% of company-owned stores were on the Panera 2.0 program.

Panera expects to open 90 to 100 new cafés in 2016, with average weekly sales of $45,000 to $47,000 per café.

The company launched its Panera 2.0 campaign in April 2014. The idea was to use technology to enhance the guest experiences by adding new digital ordering and payment options to reduce wait times, improve order accuracy and ease overcrowding in the cafés. In addition, the company made some physical changes to the kitchens to make certain operations more efficient.

These changes have definitely helped. On a two-year stacked-comp basis, the company-owned cafés saw same-store sales rise 7.2%. Two-year comps for franchise-operated cafés increased 2.0%, and company-wide sales increased 4.5%.

"While quarter-to-quarter volatility certainly does occur in the restaurant space, we view Panera as well-positioned to buck the larger trend given its continued transformation courtesy of the Panera 2.0 initiative," wrote Jim Cramer, TheStreet's founder and manager of the Action Alerts PLUS portfolio, and Research Director Jack Mohr. The portfolio owns Panera stock. "The company has proven its ability to out-execute its peers," Cramer continued in his weekly roundup on Action Alerts PLUS stocks. Cramer and Mohr have set a price target of $235 for the stock; it has recently been trading below the $190 mark.

Panera Bread is a holding in Jim Cramer's Action Alerts PLUS Charitable Trust Portfolio. Want to be alerted before Cramer buys or sells PNRA? Learn more now.

While the new technology has enhanced the customer experience and same-store sales are up, in my opinion, the company has almost no operating leverage. All of these changes are helping the top line but not the bottom line.

For example, 2016 total revenue is expected to be up about 4.3% to $2.8 billion, but operating margin will be just 9%. In 2013, without Panera 2.0, the company had a 13% operating margin. The culprit has been higher labor costs. In 2013, labor was 29.7%, as a percentage of restaurant sales. But, by the end of the year, labor is expected to be 32.4% of restaurant sales. Higher wages are wrecking the bottom line.

The average check growth was comprised of retail price increases of 2.4% and positive mix impact of 2.5%. The growth in the average check is not enough to drive earnings per share.

In this scenario, I think it's going to be hard to make any significant dough in this stock.

This article is commentary by an independent contributor. At the time of publication, the author held no positions in the stocks mentioned.