Earlier quoted context omitted.
Do you have more info on what is wrong with the markup? From the comment all I can make out is those are normal bootstrap constructs (span6 being a grid span). I'd like to fix the issues you are having (though this new version has even cleaner exported markup).
What's wrong with the markup is that it conforms to the Bootstrap documentation, and the way the Bootstrap docs recommend writing HTML is absolute garbage . is the spacer.gif of my generation.
What would be super-awesome would be a version of Jetstrap that is framework-agnostic - i.e. one in which the available classes and their suggested structure is customisable. That sounds like a much harder problem to solve, but probably one that's worth someone doing.