Hi!
There might be something else as well. I have tried a few bootstrap powered themes, but haven’t experienced issues.
My first suggestion would be to change the Javascript Source option on the Compatibility Settings submenu: http://i.imgur.com/sRJUDzZ.png
Try all the 4 options, one of them might work. On the same page there are 3 other options as well, which you can try to turn off: Load the polaroid gallery JS?, Load the isotope JS?, Load the NoUI slider JS?
If none of this works, then if you have an url where I can check the conflict, then I might be able to tell what’s exactly causing it.