Recently we ran into the issue documented here: http://www.sitepoint.com/forums/showthread.php?900027-403-error-in-chrome-with-empty-search-string
We still wanted to be able to filter dangerous URL strings, so instead of turning off that feature, we wanted to just change the generated rules.
To fix this we added:
$rules = apply_filters('better_wp_security_htaccess_rules', $rules, $bwpsserver);
It'd be nice if you added this to the actual plugin, so for those of us who need to make modifications to the htaccess for any number of reasons can, without having to modify the plugin.