Thank you for your post.
I am unable to replicate the issue with FileMaker Pro Advanced 14.0.4 on my Windows 7 machine. These are the steps I took:
1. I created a layout with a Text field. The default Theme is Enlightened.
2. I formatted the Text field to be a Checkbox and created a new value list with the two values "Yes" and "No".
3. In the Inspector, I switched to the Appearance tab.
4. With the Checkbox field selected, I changed from the "Checkbox Set" to "Checkbox Set: Checkbox".
5. Under Graphic, I set Fill to "Solid Color", and then changed the color to Red.
Let me know what I'm doing differently than you so I can replicate the issue.