So I am setting up a Quick Fields session and using Auto-OMR. The machine has QF Context, if that helps out with what features I have, maybe things arent grouping properly because I do not have the Document Classification add-on for this installation.

I add the Auto-OMR process to the Page Processing section, then  I add a master form, and then click "Add" to add a collection. Here's what I do:

1. Name my Collection and Selection at the bottom "Next: Grouping"
2. I select "Group" and then proceed to "Token Name Format"
3. I keep the Token Name Format the same as the default, as I can always change this later
4. Starting count stays at '1' and then I click "Next: Search"
5. I move the Blue field around a vertical checkbox group. There are 12 potential checkboxes. I have included a sample image of what I configure below (Figure 1)
6. I then click "Search" and get returned 12 groups. You can see this in Figure 2
7. I then click "Next: Token Values" and I find that I only have two options for the field, since it's not properly grouped the fields like it should. (Figure 3)

What am I doing wrong? 

Figure 1:

Figure 2:

Figure 3: