If there is a problem with the display of the theme, it could be from any of these:
- A jQuery conflict, where the theme is loading an old version (BD uses the loaded version from WP or whatever the theme pulls in, so the theme must do the "right thing" here for us to work)
- Improper HTML, such as unclosed tags, unmatched tags, or oddly structured things with invalid properties (this can be verified using an HTML validator on a blank page where you check the output to see if it's OK)
But whichever it is, you'll need to bring that to the theme developer's attention, since we don't have the bandwidth to support 3rd party themes. Alternately, you can hire a developer to take a closer look. We write BD with theme compatibility in mind and follow all recommended best practices for using the WP API, and that's why it's working with TwentyTwelve just fine.