Sorry for the late response, but I think it'll be worth the wait. The visual weirdness you describe has been bugging us for a while and we're working on getting a better, more useful, responsive popup window for the documentation.
We have a Work-In-Progress version on our GitHub project here: https://github.com/filipstefansson/bootstrap-3-shortcodes and I just added the first attempt at this new popup tonight! These changes will make their way to the WordPress plugin repository once they're more heavily tested, but you can grab them from GitHub right now and try them out yourself.
Thanks for your patience on this issue, and we hope you'll like the changes we've made!
Let me know if there's anything else we can help with and thanks for using this plugin!