I take that back. I just saw the new Feb '15 presentation and Chipotle has been removed from both the customers slide and the services/standards list.
I believe the answer on today's call was specific to the pork issue at Chipotle's supplier.
Chipotle has often been cited in WFCF's investor presentations. Here's a link: http://www.wherefoodcomesfrom.com/Downloads/WFCF-Oct14.pdf
See slide 6 (reference to the Chipotle Animal Welfare Standard) and slide 8 (Chipotle is on the customer list).