Hi Joel,
I set up google forms and autocrat to complete teacher informal observations for my district and had the same issue you did. I ended up creating a work around solution that works pretty well, it's not something autocrat itself does but rather some manipulation to the google sheet that collects the responses from the google form. What you need to do is separate your checkbox column into individual columns in order to be able to successfully merge them one by one into your google doc.
Here are some directions.
1. In your form responses sheet create a new sheet - let's name this Sheet 2.
2. In Sheet 2 on cell A1 you will enter formula =query('Form Responses 1'!A:R) this assumes that your responses are being collected in the 'Form Responses 1' sheet and only in columns A-R. This formula essentially copies over everything from the form responses sheet to your new sheet and updates it every time a new form is submitted.
3. Let's say column I is your Race/Ethnicity checkbox question. Starting on the next empty column of sheet 2 (in this example column S) you can start separating the column I into individual columns. To do so make the next few columns headers the names of each category in the checkbox - make sure these are exactly the same as they are in your form. In S1 we'll enter Hispanic/Latino, T1 we'll enter White, etc.
4. Now we'll enter a formula that will read column's I data and determine if the specific race/ethnicity was selected. To do so enter the following formula in S2 for the Hispanic/Latino column: =IF(ISNUMBER(SEARCH(S$1,$I2)),"X",""). This formula is searching for the data in cell S1 in cell I2, if it finds it the formula will return an X if it doesn't the formula returns a blank. You can copy cell S2 and paste in in cell T2 and the formula will automatically update to read T1 from I2. You will follow these steps 3-4 for every checkbox that can be selected.
5. When you are done entering your formulas select the cells that have the formulas and copy them down. If you expect to have about 100 responses, copy them down to row 150. Copy the formula down further than what you think you will need, because if a form is submitted and the formula wasn't copied to that row your google doc will return with empty check boxes.
6. Now when you set up autocrat set it up using sheet2 and not the Form Responses sheet. For the checkbox categories select the newly created columns, if the student selected that checkbox an X will be placed there.
We've been completing teacher informal walktrhoughs using this system for 3 years and it's worked really well. Hope this is helpful, but if you need further assistance feel free to email me directly.