@vmcmillian ...
Could you try something for me? Above the RCE (Rich Content Editor) for the Fill in Multiple Blanks question, there is an example of how to format the question:
Roses are [color1], violets are [color2]
Could you paste this text into the RCE and see if it gives you a drop-down list with color1 and color2 so that you can input possible answers? I tried this in my own sandbox course, and it works as expected. If the above example works, then is there something in your question that doesn't quite look like the "Roses" question?
Just trying to narrow down and eliminate some possibilities...thanks!