While doing a code inspection looking for something else, I came across this in notifications_views/notifications_views_handler_field_body:

    // The filter is applied now only once
    if ($method_info['filter']) {
      return check_markup($value, $filter, FALSE);
    }

PHP has so much **magic** this is probably intentional (and thus you have my apologies for the red herring), but the variable $filter is not defined anywhere in the method, module, the class being defined, nor its super class.
If I understand correctly (and I probably don't), notifications is trying to apply the filter set in Messaging Method settings, so...

    // The filter is applied now only once
    if ($method_info['filter']) {
      return check_markup($value, $method_info['filter'], FALSE);
    }

I don't have a bug for this - it just stuck me wrong, so I thought I'd report it. Apologies in advance if I've missed something obvious (which seems likely, as this piece of code has been around a while :-)