Jquery not affecting custom fields of an activity
In some CiviCRM pages/forms custom fields are loaded/reloaded via AJAX (you will notice that if you have a set of custom fields based on Activity type, the custom fields update/reload when changing the Activity type to show its correspondent set of custom field).

With that in mind you should trigger you script on .ajaxComplete(), something along those lines:

CRM.$( function( $ ) {
    $( document ).ajaxComplete( function( event, xhr, settings ) { // optional params if you need to differenciate between events/requests
        // do stuff
    }
} )