Filters gone after 1.6 update

Can you please give a link to your products listing and a screenshot of the Display tab of the configuration ?

Indeed, for existing modules and menus, the new option default value is not set so you need to save once the options.

You can edit the file "listing" of the view "product" via the menu Display->Views and change the line:
$display_filters = $this->params->get('display_filters');

to:
$display_filters = $this->params->get('display_filters', -1);

and that should avoid the problem.