I don’t think there is a flag. I think FlashBuilder edits the html template based on project properties. The inclusion of history.js is commented out by default in the template.
I thought the same thing, but these two lines are definitely uncommented in the wrapper's source:
<!-- BEGIN Browser History required section -->
<link rel="stylesheet" type="text/css" href="history/history.css" />
<!-- END Browser History required section -->
The URL change are successfully written from the swf to the location bar, but not backwards.
Ah. Bizarrely our build wasn't putting the correct swf name into the three places it's referenced in the wrapper, and that was somehow messing it up. Making sure all of them were correct fixed the problem. Thanks!