@educause ,  You almost certainly have either figured out an answer to your question above or found a work-around. This question in the Qualtrics system is quite old! But since you never got anyone to reply to your question, I thought I would give it a try. 

-- Have you double checked the configuration of the question export tags for the checkbox grid columns? Make sure that each column in the grid has a unique export tag assigned to it. If the export tags are not set correctly or are conflicting, it could cause unexpected behavior when retrieving the survey data.

-- Have you verified the parameters you are using when making the API call to retrieve the survey JSON? Ensure that you are including the necessary parameters to fetch all the columns in the checkbox grid. Review the Qualtrics API documentation for the specific parameters required to retrieve grid data.

-- Check if you are using the most up-to-date version of the Qualtrics API. It's possible that there might be a bug or compatibility issue with the version you are currently using.

--If all this fails, I would reach out to Qualtrics support for help.