If you don't really need the element to be invisible (ie take up the space) tho you might wanna redefine .hidden (in you local css, don't change bootstrap source, or even better, in your local LESS file).
Then I had another problem, since my application generates new elements and append/prepend them. What I finally did is after genereting the new element I do:
var newEl = ...;
$(newEl).find('.hidden').hide().removeClass('hidden');