Changing the colour scheme only changes the CSS used, not the HTML of the page, so shouldn't affect whether includelets appear. I've tried Bootstrap theme with the Superhero colour scheme on a few sites and the right column is working fine for me!

It also seems to be OK on your site when I look at it now.

Are you still having problems? If so can you be more specific about which page the problem appears with, and which browser you're using, and anything else you think might be important for me to see the problem.